diff --git a/apps/neuroglancer-url/src/data.ts b/apps/neuroglancer-url/src/data.ts
index 40311c0..f82b5e8 100644
--- a/apps/neuroglancer-url/src/data.ts
+++ b/apps/neuroglancer-url/src/data.ts
@@ -1,349 +1,309 @@
-import type { NGData } from "./types";
+import type { NGData } from './types';
export const data: NGData[] = [
{
- "function": "get_image_series_grid_url",
- "params": {
- "src_config_list": [
- {
- "blue_max": 4095.0,
- "blue_min": 0.0,
- "green_max": 7261.0,
- "green_min": 0.0,
- "img_name": "1125628029 (40_512_512)",
- "ome_zarr_shape": [
- 3,
- 142,
- 29998,
- 39998
+ function: 'get_image_series_grid_url',
+ params: {
+ src_config_list: [
+ {
+ blue_max: 4095.0,
+ blue_min: 0.0,
+ green_max: 7261.0,
+ green_min: 0.0,
+ img_name: '1125628029 (40_512_512)',
+ ome_zarr_shape: [3, 142, 29998, 39998],
+ red_max: 1261.0,
+ red_min: 0.0,
+ src_url: 'zarr://s3://tissuecyte-ome-zarr-poc/40_128_128/1125628029',
+ x_mm: 0.00035,
+ y_mm: 0.00035,
+ z_mm: 0.1,
+ },
+ {
+ blue_max: 4095.0,
+ blue_min: 0.0,
+ green_max: 1304.0,
+ green_min: 0.0,
+ img_name: '1145081396 (40_512_512)',
+ ome_zarr_shape: [3, 142, 11998, 15998],
+ red_max: 1344.0,
+ red_min: 0.0,
+ src_url: 'zarr://s3://tissuecyte-ome-zarr-poc/40_128_128/1145081396',
+ x_mm: 0.000875,
+ y_mm: 0.000875,
+ z_mm: 0.1,
+ },
+ {
+ blue_max: 4095.0,
+ blue_min: 0.0,
+ green_max: 4045.0,
+ green_min: 0.0,
+ img_name: '1182837942 (40_512_512)',
+ ome_zarr_shape: [3, 142, 29998, 39998],
+ red_max: 864.0,
+ red_min: 0.0,
+ src_url: 'zarr://s3://tissuecyte-ome-zarr-poc/40_128_128/1182837942',
+ x_mm: 0.00035,
+ y_mm: 0.00035,
+ z_mm: 0.1,
+ },
+ {
+ blue_max: 4095.0,
+ blue_min: 0.0,
+ green_max: 3013.0,
+ green_min: 0.0,
+ img_name: '1240649363 (40_512_512)',
+ ome_zarr_shape: [3, 142, 29998, 39998],
+ red_max: 1356.0,
+ red_min: 0.0,
+ src_url: 'zarr://s3://tissuecyte-ome-zarr-poc/40_128_128/1240649363',
+ x_mm: 0.00035,
+ y_mm: 0.00035,
+ z_mm: 0.1,
+ },
],
- "red_max": 1261.0,
- "red_min": 0.0,
- "src_url": "zarr://s3://tissuecyte-ome-zarr-poc/40_128_128/1125628029",
- "x_mm": 0.00035,
- "y_mm": 0.00035,
- "z_mm": 0.1
- },
- {
- "blue_max": 4095.0,
- "blue_min": 0.0,
- "green_max": 1304.0,
- "green_min": 0.0,
- "img_name": "1145081396 (40_512_512)",
- "ome_zarr_shape": [
- 3,
- 142,
- 11998,
- 15998
- ],
- "red_max": 1344.0,
- "red_min": 0.0,
- "src_url": "zarr://s3://tissuecyte-ome-zarr-poc/40_128_128/1145081396",
- "x_mm": 0.000875,
- "y_mm": 0.000875,
- "z_mm": 0.1
- },
- {
- "blue_max": 4095.0,
- "blue_min": 0.0,
- "green_max": 4045.0,
- "green_min": 0.0,
- "img_name": "1182837942 (40_512_512)",
- "ome_zarr_shape": [
- 3,
- 142,
- 29998,
- 39998
- ],
- "red_max": 864.0,
- "red_min": 0.0,
- "src_url": "zarr://s3://tissuecyte-ome-zarr-poc/40_128_128/1182837942",
- "x_mm": 0.00035,
- "y_mm": 0.00035,
- "z_mm": 0.1
- },
- {
- "blue_max": 4095.0,
- "blue_min": 0.0,
- "green_max": 3013.0,
- "green_min": 0.0,
- "img_name": "1240649363 (40_512_512)",
- "ome_zarr_shape": [
- 3,
- 142,
- 29998,
- 39998
- ],
- "red_max": 1356.0,
- "red_min": 0.0,
- "src_url": "zarr://s3://tissuecyte-ome-zarr-poc/40_128_128/1240649363",
- "x_mm": 0.00035,
- "y_mm": 0.00035,
- "z_mm": 0.1
- }
- ]
- },
- "type": "Multiple image series; coronal projection",
- "url": 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+ },
+ type: 'Multiple image series; coronal projection',
+ url: 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},
{
- "function": "get_neuroglancer_url",
- "params": {
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- },
- "type": "Single image series; all three planes",
- "url": "https://neuroglancer-demo.appspot.com/#!%7B%22dimensions%22%3A%20%7B%22x%22%3A%20%5B3.5e-07%2C%20%22m%22%5D%2C%20%22y%22%3A%20%5B3.5e-07%2C%20%22m%22%5D%2C%20%22z%22%3A%20%5B0.0001%2C%20%22m%22%5D%7D%2C%20%22crossSectionScale%22%3A%2057.142857142857146%2C%20%22projectionScale%22%3A%2040000%2C%20%22selectedLayer%22%3A%20%7B%22visible%22%3A%20true%2C%20%22layer%22%3A%20%221125628029%20%2840_128_128%29%22%7D%2C%20%22layout%22%3A%20%224panel%22%2C%20%22layers%22%3A%20%5B%7B%22type%22%3A%20%22image%22%2C%20%22tab%22%3A%20%22rendering%22%2C%20%22shader%22%3A%20%22%5Cn%20%20%20%20%23uicontrol%20float%20red_min%20slider%28min%3D0.0%2C%20max%3D2522.0%29%5Cn%20%20%20%20%23uicontrol%20float%20red_max%20slider%28min%3D0.0%2C%20max%3D2522.0%29%5Cn%20%20%20%20%23uicontrol%20float%20green_min%20slider%28min%3D0.0%2C%20max%3D14522.0%29%5Cn%20%20%20%20%23uicontrol%20float%20green_max%20slider%28min%3D0.0%2C%20max%3D14522.0%29%5Cn%20%20%20%20%23uicontrol%20float%20blue_min%20slider%28min%3D0.0%2C%20max%3D8190.0%29%5Cn%20%20%20%20%23uicontrol%20float%20blue_max%20slider%28min%3D0.0%2C%20max%3D8190.0%29%5Cn%20%20%20%20%23uicontrol%20bool%20red_visible%20checkbox%28default%3Dtrue%29%3B%5Cn%20%20%20%20%23uicontrol%20bool%20green_visible%20checkbox%28default%3Dtrue%29%3B%5Cn%20%20%20%20%23uicontrol%20bool%20blue_visible%20checkbox%28default%3Dtrue%29%3B%5Cn%20%20%20%20%5Cn%20%20%20%20void%20main%28%29%20%7B%5Cn%20%20%20%20%20%20%20%20float%20r%3B%5Cn%20%20%20%20%20%20%20%20float%20r_scale%3Dred_max-red_min%3B%5Cn%20%20%20%20%20%20%20%20if%28%21red_visible%20%7C%7C%20%28r_scale%3C%3D0.0%29%20%29%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20r%3D0.0%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20else%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20r%3D%28float%28getDataValue%280%29.value%29-red_min%29/r_scale%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20if%28r%3E1.0%29r%3D1.0%3B%5Cn%5Cn%20%20%20%20%20%20%20%20%20float%20g%3B%5Cn%20%20%20%20%20%20%20%20%20float%20g_scale%3Dgreen_max-green_min%3B%5Cn%20%20%20%20%20%20%20%20%20if%28%21green_visible%20%7C%7C%20%28g_scale%3C%3D0.0%29%29%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20g%3D0.0%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20else%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20g%3D%28float%28getDataValue%281%29.value%29-green_min%29/g_scale%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20if%28g%3E1.0%29g%3D1.0%3B%5Cn%5Cn%20%20%20%20%20%20%20%20%20float%20b%3B%5Cn%20%20%20%20%20%20%20%20%20float%20b_scale%3Dblue_max-blue_min%3B%5Cn%20%20%20%20%20%20%20%20%20if%28%21blue_visible%20%7C%7C%20%28b_scale%3C%3D0.0%29%29%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20b%3D0.0%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20else%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20b%3D%28float%28getDataValue%282%29.value%29-blue_min%29/b_scale%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20if%28b%3E1.0%29b%3D1.0%3B%5Cn%5Cn%20%20%20%20%20%20%20%20%20emitRGB%28vec3%28r%2Cg%2Cb%29%29%3B%5Cn%20%20%20%20%20%7D%5Cn%20%20%20%20%20%22%2C%20%22shaderControls%22%3A%20%7B%22red_min%22%3A%200.0%2C%20%22red_max%22%3A%201261.0%2C%20%22green_min%22%3A%200.0%2C%20%22green_max%22%3A%207261.0%2C%20%22blue_min%22%3A%200.0%2C%20%22blue_max%22%3A%204095.0%7D%2C%20%22source%22%3A%20%7B%22url%22%3A%20%22zarr%3A//s3%3A//tissuecyte-ome-zarr-poc/40_128_128/1125628029%22%2C%20%22transform%22%3A%20%7B%22outputDimensions%22%3A%20%7B%22c%5E%22%3A%20%5B1%2C%20%22%22%5D%2C%20%22z%22%3A%20%5B0.0001%2C%20%22m%22%5D%2C%20%22y%22%3A%20%5B3.5e-07%2C%20%22m%22%5D%2C%20%22x%22%3A%20%5B3.5e-07%2C%20%22m%22%5D%7D%7D%7D%2C%20%22channelDimensions%22%3A%20%7B%22c%5E%22%3A%20%5B1%2C%20%22%22%5D%7D%2C%20%22name%22%3A%20%221125628029%20%2840_128_128%29%22%2C%20%22opacity%22%3A%201%7D%5D%7D"
+ function: 'get_neuroglancer_url',
+ params: {
+ blue_max: 4095.0,
+ blue_min: 0.0,
+ cross_section_scale: 57.142857142857146,
+ green_max: 7261.0,
+ green_min: 0.0,
+ img_name: '1125628029 (40_128_128)',
+ layout: '4panel',
+ red_max: 1261.0,
+ red_min: 0.0,
+ src_url: 'zarr://s3://tissuecyte-ome-zarr-poc/40_128_128/1125628029',
+ x_mm: 0.00035,
+ y_mm: 0.00035,
+ z_mm: 0.1,
+ },
+ type: 'Single image series; all three planes',
+ url: 'https://neuroglancer-demo.appspot.com/#!%7B%22dimensions%22%3A%20%7B%22x%22%3A%20%5B3.5e-07%2C%20%22m%22%5D%2C%20%22y%22%3A%20%5B3.5e-07%2C%20%22m%22%5D%2C%20%22z%22%3A%20%5B0.0001%2C%20%22m%22%5D%7D%2C%20%22crossSectionScale%22%3A%2057.142857142857146%2C%20%22projectionScale%22%3A%2040000%2C%20%22selectedLayer%22%3A%20%7B%22visible%22%3A%20true%2C%20%22layer%22%3A%20%221125628029%20%2840_128_128%29%22%7D%2C%20%22layout%22%3A%20%224panel%22%2C%20%22layers%22%3A%20%5B%7B%22type%22%3A%20%22image%22%2C%20%22tab%22%3A%20%22rendering%22%2C%20%22shader%22%3A%20%22%5Cn%20%20%20%20%23uicontrol%20float%20red_min%20slider%28min%3D0.0%2C%20max%3D2522.0%29%5Cn%20%20%20%20%23uicontrol%20float%20red_max%20slider%28min%3D0.0%2C%20max%3D2522.0%29%5Cn%20%20%20%20%23uicontrol%20float%20green_min%20slider%28min%3D0.0%2C%20max%3D14522.0%29%5Cn%20%20%20%20%23uicontrol%20float%20green_max%20slider%28min%3D0.0%2C%20max%3D14522.0%29%5Cn%20%20%20%20%23uicontrol%20float%20blue_min%20slider%28min%3D0.0%2C%20max%3D8190.0%29%5Cn%20%20%20%20%23uicontrol%20float%20blue_max%20slider%28min%3D0.0%2C%20max%3D8190.0%29%5Cn%20%20%20%20%23uicontrol%20bool%20red_visible%20checkbox%28default%3Dtrue%29%3B%5Cn%20%20%20%20%23uicontrol%20bool%20green_visible%20checkbox%28default%3Dtrue%29%3B%5Cn%20%20%20%20%23uicontrol%20bool%20blue_visible%20checkbox%28default%3Dtrue%29%3B%5Cn%20%20%20%20%5Cn%20%20%20%20void%20main%28%29%20%7B%5Cn%20%20%20%20%20%20%20%20float%20r%3B%5Cn%20%20%20%20%20%20%20%20float%20r_scale%3Dred_max-red_min%3B%5Cn%20%20%20%20%20%20%20%20if%28%21red_visible%20%7C%7C%20%28r_scale%3C%3D0.0%29%20%29%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20r%3D0.0%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20else%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20r%3D%28float%28getDataValue%280%29.value%29-red_min%29/r_scale%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20if%28r%3E1.0%29r%3D1.0%3B%5Cn%5Cn%20%20%20%20%20%20%20%20%20float%20g%3B%5Cn%20%20%20%20%20%20%20%20%20float%20g_scale%3Dgreen_max-green_min%3B%5Cn%20%20%20%20%20%20%20%20%20if%28%21green_visible%20%7C%7C%20%28g_scale%3C%3D0.0%29%29%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20g%3D0.0%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20else%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20g%3D%28float%28getDataValue%281%29.value%29-green_min%29/g_scale%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20if%28g%3E1.0%29g%3D1.0%3B%5Cn%5Cn%20%20%20%20%20%20%20%20%20float%20b%3B%5Cn%20%20%20%20%20%20%20%20%20float%20b_scale%3Dblue_max-blue_min%3B%5Cn%20%20%20%20%20%20%20%20%20if%28%21blue_visible%20%7C%7C%20%28b_scale%3C%3D0.0%29%29%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20b%3D0.0%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20else%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20b%3D%28float%28getDataValue%282%29.value%29-blue_min%29/b_scale%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20if%28b%3E1.0%29b%3D1.0%3B%5Cn%5Cn%20%20%20%20%20%20%20%20%20emitRGB%28vec3%28r%2Cg%2Cb%29%29%3B%5Cn%20%20%20%20%20%7D%5Cn%20%20%20%20%20%22%2C%20%22shaderControls%22%3A%20%7B%22red_min%22%3A%200.0%2C%20%22red_max%22%3A%201261.0%2C%20%22green_min%22%3A%200.0%2C%20%22green_max%22%3A%207261.0%2C%20%22blue_min%22%3A%200.0%2C%20%22blue_max%22%3A%204095.0%7D%2C%20%22source%22%3A%20%7B%22url%22%3A%20%22zarr%3A//s3%3A//tissuecyte-ome-zarr-poc/40_128_128/1125628029%22%2C%20%22transform%22%3A%20%7B%22outputDimensions%22%3A%20%7B%22c%5E%22%3A%20%5B1%2C%20%22%22%5D%2C%20%22z%22%3A%20%5B0.0001%2C%20%22m%22%5D%2C%20%22y%22%3A%20%5B3.5e-07%2C%20%22m%22%5D%2C%20%22x%22%3A%20%5B3.5e-07%2C%20%22m%22%5D%7D%7D%7D%2C%20%22channelDimensions%22%3A%20%7B%22c%5E%22%3A%20%5B1%2C%20%22%22%5D%7D%2C%20%22name%22%3A%20%221125628029%20%2840_128_128%29%22%2C%20%22opacity%22%3A%201%7D%5D%7D',
},
{
- "function": "get_neuroglancer_url",
- "params": {
- "blue_max": 4095.0,
- "blue_min": 0.0,
- "cross_section_scale": 37.714285714285715,
- "green_max": 7261.0,
- "green_min": 0.0,
- "img_name": "1125628029 (40_128_128)",
- "layout": "xy",
- "red_max": 1261.0,
- "red_min": 0.0,
- "src_url": "zarr://s3://tissuecyte-ome-zarr-poc/40_128_128/1125628029",
- "x_mm": 0.00035,
- "y_mm": 0.00035,
- "z_mm": 0.1
- },
- "type": "Single image series; coronal projection",
- "url": "https://neuroglancer-demo.appspot.com/#!%7B%22dimensions%22%3A%20%7B%22x%22%3A%20%5B3.5e-07%2C%20%22m%22%5D%2C%20%22y%22%3A%20%5B3.5e-07%2C%20%22m%22%5D%2C%20%22z%22%3A%20%5B0.0001%2C%20%22m%22%5D%7D%2C%20%22crossSectionScale%22%3A%2037.714285714285715%2C%20%22projectionScale%22%3A%2040000%2C%20%22selectedLayer%22%3A%20%7B%22visible%22%3A%20true%2C%20%22layer%22%3A%20%221125628029%20%2840_128_128%29%22%7D%2C%20%22layout%22%3A%20%22xy%22%2C%20%22layers%22%3A%20%5B%7B%22type%22%3A%20%22image%22%2C%20%22tab%22%3A%20%22rendering%22%2C%20%22shader%22%3A%20%22%5Cn%20%20%20%20%23uicontrol%20float%20red_min%20slider%28min%3D0.0%2C%20max%3D2522.0%29%5Cn%20%20%20%20%23uicontrol%20float%20red_max%20slider%28min%3D0.0%2C%20max%3D2522.0%29%5Cn%20%20%20%20%23uicontrol%20float%20green_min%20slider%28min%3D0.0%2C%20max%3D14522.0%29%5Cn%20%20%20%20%23uicontrol%20float%20green_max%20slider%28min%3D0.0%2C%20max%3D14522.0%29%5Cn%20%20%20%20%23uicontrol%20float%20blue_min%20slider%28min%3D0.0%2C%20max%3D8190.0%29%5Cn%20%20%20%20%23uicontrol%20float%20blue_max%20slider%28min%3D0.0%2C%20max%3D8190.0%29%5Cn%20%20%20%20%23uicontrol%20bool%20red_visible%20checkbox%28default%3Dtrue%29%3B%5Cn%20%20%20%20%23uicontrol%20bool%20green_visible%20checkbox%28default%3Dtrue%29%3B%5Cn%20%20%20%20%23uicontrol%20bool%20blue_visible%20checkbox%28default%3Dtrue%29%3B%5Cn%20%20%20%20%5Cn%20%20%20%20void%20main%28%29%20%7B%5Cn%20%20%20%20%20%20%20%20float%20r%3B%5Cn%20%20%20%20%20%20%20%20float%20r_scale%3Dred_max-red_min%3B%5Cn%20%20%20%20%20%20%20%20if%28%21red_visible%20%7C%7C%20%28r_scale%3C%3D0.0%29%20%29%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20r%3D0.0%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20else%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20r%3D%28float%28getDataValue%280%29.value%29-red_min%29/r_scale%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20if%28r%3E1.0%29r%3D1.0%3B%5Cn%5Cn%20%20%20%20%20%20%20%20%20float%20g%3B%5Cn%20%20%20%20%20%20%20%20%20float%20g_scale%3Dgreen_max-green_min%3B%5Cn%20%20%20%20%20%20%20%20%20if%28%21green_visible%20%7C%7C%20%28g_scale%3C%3D0.0%29%29%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20g%3D0.0%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20else%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20g%3D%28float%28getDataValue%281%29.value%29-green_min%29/g_scale%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20if%28g%3E1.0%29g%3D1.0%3B%5Cn%5Cn%20%20%20%20%20%20%20%20%20float%20b%3B%5Cn%20%20%20%20%20%20%20%20%20float%20b_scale%3Dblue_max-blue_min%3B%5Cn%20%20%20%20%20%20%20%20%20if%28%21blue_visible%20%7C%7C%20%28b_scale%3C%3D0.0%29%29%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20b%3D0.0%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20else%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20b%3D%28float%28getDataValue%282%29.value%29-blue_min%29/b_scale%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20if%28b%3E1.0%29b%3D1.0%3B%5Cn%5Cn%20%20%20%20%20%20%20%20%20emitRGB%28vec3%28r%2Cg%2Cb%29%29%3B%5Cn%20%20%20%20%20%7D%5Cn%20%20%20%20%20%22%2C%20%22shaderControls%22%3A%20%7B%22red_min%22%3A%200.0%2C%20%22red_max%22%3A%201261.0%2C%20%22green_min%22%3A%200.0%2C%20%22green_max%22%3A%207261.0%2C%20%22blue_min%22%3A%200.0%2C%20%22blue_max%22%3A%204095.0%7D%2C%20%22source%22%3A%20%7B%22url%22%3A%20%22zarr%3A//s3%3A//tissuecyte-ome-zarr-poc/40_128_128/1125628029%22%2C%20%22transform%22%3A%20%7B%22outputDimensions%22%3A%20%7B%22c%5E%22%3A%20%5B1%2C%20%22%22%5D%2C%20%22z%22%3A%20%5B0.0001%2C%20%22m%22%5D%2C%20%22y%22%3A%20%5B3.5e-07%2C%20%22m%22%5D%2C%20%22x%22%3A%20%5B3.5e-07%2C%20%22m%22%5D%7D%7D%7D%2C%20%22channelDimensions%22%3A%20%7B%22c%5E%22%3A%20%5B1%2C%20%22%22%5D%7D%2C%20%22name%22%3A%20%221125628029%20%2840_128_128%29%22%2C%20%22opacity%22%3A%201%7D%5D%7D"
+ function: 'get_neuroglancer_url',
+ params: {
+ blue_max: 4095.0,
+ blue_min: 0.0,
+ cross_section_scale: 37.714285714285715,
+ green_max: 7261.0,
+ green_min: 0.0,
+ img_name: '1125628029 (40_128_128)',
+ layout: 'xy',
+ red_max: 1261.0,
+ red_min: 0.0,
+ src_url: 'zarr://s3://tissuecyte-ome-zarr-poc/40_128_128/1125628029',
+ x_mm: 0.00035,
+ y_mm: 0.00035,
+ z_mm: 0.1,
+ },
+ type: 'Single image series; coronal projection',
+ url: 'https://neuroglancer-demo.appspot.com/#!%7B%22dimensions%22%3A%20%7B%22x%22%3A%20%5B3.5e-07%2C%20%22m%22%5D%2C%20%22y%22%3A%20%5B3.5e-07%2C%20%22m%22%5D%2C%20%22z%22%3A%20%5B0.0001%2C%20%22m%22%5D%7D%2C%20%22crossSectionScale%22%3A%2037.714285714285715%2C%20%22projectionScale%22%3A%2040000%2C%20%22selectedLayer%22%3A%20%7B%22visible%22%3A%20true%2C%20%22layer%22%3A%20%221125628029%20%2840_128_128%29%22%7D%2C%20%22layout%22%3A%20%22xy%22%2C%20%22layers%22%3A%20%5B%7B%22type%22%3A%20%22image%22%2C%20%22tab%22%3A%20%22rendering%22%2C%20%22shader%22%3A%20%22%5Cn%20%20%20%20%23uicontrol%20float%20red_min%20slider%28min%3D0.0%2C%20max%3D2522.0%29%5Cn%20%20%20%20%23uicontrol%20float%20red_max%20slider%28min%3D0.0%2C%20max%3D2522.0%29%5Cn%20%20%20%20%23uicontrol%20float%20green_min%20slider%28min%3D0.0%2C%20max%3D14522.0%29%5Cn%20%20%20%20%23uicontrol%20float%20green_max%20slider%28min%3D0.0%2C%20max%3D14522.0%29%5Cn%20%20%20%20%23uicontrol%20float%20blue_min%20slider%28min%3D0.0%2C%20max%3D8190.0%29%5Cn%20%20%20%20%23uicontrol%20float%20blue_max%20slider%28min%3D0.0%2C%20max%3D8190.0%29%5Cn%20%20%20%20%23uicontrol%20bool%20red_visible%20checkbox%28default%3Dtrue%29%3B%5Cn%20%20%20%20%23uicontrol%20bool%20green_visible%20checkbox%28default%3Dtrue%29%3B%5Cn%20%20%20%20%23uicontrol%20bool%20blue_visible%20checkbox%28default%3Dtrue%29%3B%5Cn%20%20%20%20%5Cn%20%20%20%20void%20main%28%29%20%7B%5Cn%20%20%20%20%20%20%20%20float%20r%3B%5Cn%20%20%20%20%20%20%20%20float%20r_scale%3Dred_max-red_min%3B%5Cn%20%20%20%20%20%20%20%20if%28%21red_visible%20%7C%7C%20%28r_scale%3C%3D0.0%29%20%29%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20r%3D0.0%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20else%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20r%3D%28float%28getDataValue%280%29.value%29-red_min%29/r_scale%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20if%28r%3E1.0%29r%3D1.0%3B%5Cn%5Cn%20%20%20%20%20%20%20%20%20float%20g%3B%5Cn%20%20%20%20%20%20%20%20%20float%20g_scale%3Dgreen_max-green_min%3B%5Cn%20%20%20%20%20%20%20%20%20if%28%21green_visible%20%7C%7C%20%28g_scale%3C%3D0.0%29%29%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20g%3D0.0%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20else%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20g%3D%28float%28getDataValue%281%29.value%29-green_min%29/g_scale%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20if%28g%3E1.0%29g%3D1.0%3B%5Cn%5Cn%20%20%20%20%20%20%20%20%20float%20b%3B%5Cn%20%20%20%20%20%20%20%20%20float%20b_scale%3Dblue_max-blue_min%3B%5Cn%20%20%20%20%20%20%20%20%20if%28%21blue_visible%20%7C%7C%20%28b_scale%3C%3D0.0%29%29%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20b%3D0.0%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20else%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20b%3D%28float%28getDataValue%282%29.value%29-blue_min%29/b_scale%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20if%28b%3E1.0%29b%3D1.0%3B%5Cn%5Cn%20%20%20%20%20%20%20%20%20emitRGB%28vec3%28r%2Cg%2Cb%29%29%3B%5Cn%20%20%20%20%20%7D%5Cn%20%20%20%20%20%22%2C%20%22shaderControls%22%3A%20%7B%22red_min%22%3A%200.0%2C%20%22red_max%22%3A%201261.0%2C%20%22green_min%22%3A%200.0%2C%20%22green_max%22%3A%207261.0%2C%20%22blue_min%22%3A%200.0%2C%20%22blue_max%22%3A%204095.0%7D%2C%20%22source%22%3A%20%7B%22url%22%3A%20%22zarr%3A//s3%3A//tissuecyte-ome-zarr-poc/40_128_128/1125628029%22%2C%20%22transform%22%3A%20%7B%22outputDimensions%22%3A%20%7B%22c%5E%22%3A%20%5B1%2C%20%22%22%5D%2C%20%22z%22%3A%20%5B0.0001%2C%20%22m%22%5D%2C%20%22y%22%3A%20%5B3.5e-07%2C%20%22m%22%5D%2C%20%22x%22%3A%20%5B3.5e-07%2C%20%22m%22%5D%7D%7D%7D%2C%20%22channelDimensions%22%3A%20%7B%22c%5E%22%3A%20%5B1%2C%20%22%22%5D%7D%2C%20%22name%22%3A%20%221125628029%20%2840_128_128%29%22%2C%20%22opacity%22%3A%201%7D%5D%7D',
},
{
- "function": "get_contact_sheet_url",
- "params": {
- "blue_max": 4095.0,
- "blue_min": 0.0,
- "cross_section_scale": 576.0,
- "green_max": 7261.0,
- "green_min": 0.0,
- "img_name": "1125628029 (40_128_128)",
- "ome_zarr_shape": [
- 3,
- 142,
- 29998,
- 39998
- ],
- "red_max": 1261.0,
- "red_min": 0.0,
- "src_url": "zarr://s3://tissuecyte-ome-zarr-poc/40_128_128/1125628029",
- "x_mm": 0.00035,
- "y_mm": 0.00035,
- "z_mm": 0.1
- },
- "type": "Single image series; contact sheet",
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+ function: 'get_contact_sheet_url',
+ params: {
+ blue_max: 4095.0,
+ blue_min: 0.0,
+ cross_section_scale: 576.0,
+ green_max: 7261.0,
+ green_min: 0.0,
+ img_name: '1125628029 (40_128_128)',
+ ome_zarr_shape: [3, 142, 29998, 39998],
+ red_max: 1261.0,
+ red_min: 0.0,
+ src_url: 'zarr://s3://tissuecyte-ome-zarr-poc/40_128_128/1125628029',
+ x_mm: 0.00035,
+ y_mm: 0.00035,
+ z_mm: 0.1,
+ },
+ type: 'Single image series; contact sheet',
+ url: 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},
{
- "function": "get_neuroglancer_url",
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- "img_name": "1145081396 (40_128_128)",
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- "src_url": "zarr://s3://tissuecyte-ome-zarr-poc/40_128_128/1145081396",
- "x_mm": 0.000875,
- "y_mm": 0.000875,
- "z_mm": 0.1
- },
- "type": "Single image series; all three planes",
- "url": "https://neuroglancer-demo.appspot.com/#!%7B%22dimensions%22%3A%20%7B%22x%22%3A%20%5B8.75e-07%2C%20%22m%22%5D%2C%20%22y%22%3A%20%5B8.75e-07%2C%20%22m%22%5D%2C%20%22z%22%3A%20%5B0.0001%2C%20%22m%22%5D%7D%2C%20%22crossSectionScale%22%3A%2022.857142857142858%2C%20%22projectionScale%22%3A%2040000%2C%20%22selectedLayer%22%3A%20%7B%22visible%22%3A%20true%2C%20%22layer%22%3A%20%221145081396%20%2840_128_128%29%22%7D%2C%20%22layout%22%3A%20%224panel%22%2C%20%22layers%22%3A%20%5B%7B%22type%22%3A%20%22image%22%2C%20%22tab%22%3A%20%22rendering%22%2C%20%22shader%22%3A%20%22%5Cn%20%20%20%20%23uicontrol%20float%20red_min%20slider%28min%3D0.0%2C%20max%3D2688.0%29%5Cn%20%20%20%20%23uicontrol%20float%20red_max%20slider%28min%3D0.0%2C%20max%3D2688.0%29%5Cn%20%20%20%20%23uicontrol%20float%20green_min%20slider%28min%3D0.0%2C%20max%3D2608.0%29%5Cn%20%20%20%20%23uicontrol%20float%20green_max%20slider%28min%3D0.0%2C%20max%3D2608.0%29%5Cn%20%20%20%20%23uicontrol%20float%20blue_min%20slider%28min%3D0.0%2C%20max%3D8190.0%29%5Cn%20%20%20%20%23uicontrol%20float%20blue_max%20slider%28min%3D0.0%2C%20max%3D8190.0%29%5Cn%20%20%20%20%23uicontrol%20bool%20red_visible%20checkbox%28default%3Dtrue%29%3B%5Cn%20%20%20%20%23uicontrol%20bool%20green_visible%20checkbox%28default%3Dtrue%29%3B%5Cn%20%20%20%20%23uicontrol%20bool%20blue_visible%20checkbox%28default%3Dtrue%29%3B%5Cn%20%20%20%20%5Cn%20%20%20%20void%20main%28%29%20%7B%5Cn%20%20%20%20%20%20%20%20float%20r%3B%5Cn%20%20%20%20%20%20%20%20float%20r_scale%3Dred_max-red_min%3B%5Cn%20%20%20%20%20%20%20%20if%28%21red_visible%20%7C%7C%20%28r_scale%3C%3D0.0%29%20%29%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20r%3D0.0%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20else%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20r%3D%28float%28getDataValue%280%29.value%29-red_min%29/r_scale%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20if%28r%3E1.0%29r%3D1.0%3B%5Cn%5Cn%20%20%20%20%20%20%20%20%20float%20g%3B%5Cn%20%20%20%20%20%20%20%20%20float%20g_scale%3Dgreen_max-green_min%3B%5Cn%20%20%20%20%20%20%20%20%20if%28%21green_visible%20%7C%7C%20%28g_scale%3C%3D0.0%29%29%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20g%3D0.0%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20else%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20g%3D%28float%28getDataValue%281%29.value%29-green_min%29/g_scale%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20if%28g%3E1.0%29g%3D1.0%3B%5Cn%5Cn%20%20%20%20%20%20%20%20%20float%20b%3B%5Cn%20%20%20%20%20%20%20%20%20float%20b_scale%3Dblue_max-blue_min%3B%5Cn%20%20%20%20%20%20%20%20%20if%28%21blue_visible%20%7C%7C%20%28b_scale%3C%3D0.0%29%29%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20b%3D0.0%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20else%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20b%3D%28float%28getDataValue%282%29.value%29-blue_min%29/b_scale%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20if%28b%3E1.0%29b%3D1.0%3B%5Cn%5Cn%20%20%20%20%20%20%20%20%20emitRGB%28vec3%28r%2Cg%2Cb%29%29%3B%5Cn%20%20%20%20%20%7D%5Cn%20%20%20%20%20%22%2C%20%22shaderControls%22%3A%20%7B%22red_min%22%3A%200.0%2C%20%22red_max%22%3A%201344.0%2C%20%22green_min%22%3A%200.0%2C%20%22green_max%22%3A%201304.0%2C%20%22blue_min%22%3A%200.0%2C%20%22blue_max%22%3A%204095.0%7D%2C%20%22source%22%3A%20%7B%22url%22%3A%20%22zarr%3A//s3%3A//tissuecyte-ome-zarr-poc/40_128_128/1145081396%22%2C%20%22transform%22%3A%20%7B%22outputDimensions%22%3A%20%7B%22c%5E%22%3A%20%5B1%2C%20%22%22%5D%2C%20%22z%22%3A%20%5B0.0001%2C%20%22m%22%5D%2C%20%22y%22%3A%20%5B8.75e-07%2C%20%22m%22%5D%2C%20%22x%22%3A%20%5B8.75e-07%2C%20%22m%22%5D%7D%7D%7D%2C%20%22channelDimensions%22%3A%20%7B%22c%5E%22%3A%20%5B1%2C%20%22%22%5D%7D%2C%20%22name%22%3A%20%221145081396%20%2840_128_128%29%22%2C%20%22opacity%22%3A%201%7D%5D%7D"
+ function: 'get_neuroglancer_url',
+ params: {
+ blue_max: 4095.0,
+ blue_min: 0.0,
+ cross_section_scale: 22.857142857142858,
+ green_max: 1304.0,
+ green_min: 0.0,
+ img_name: '1145081396 (40_128_128)',
+ layout: '4panel',
+ red_max: 1344.0,
+ red_min: 0.0,
+ src_url: 'zarr://s3://tissuecyte-ome-zarr-poc/40_128_128/1145081396',
+ x_mm: 0.000875,
+ y_mm: 0.000875,
+ z_mm: 0.1,
+ },
+ type: 'Single image series; all three planes',
+ url: 'https://neuroglancer-demo.appspot.com/#!%7B%22dimensions%22%3A%20%7B%22x%22%3A%20%5B8.75e-07%2C%20%22m%22%5D%2C%20%22y%22%3A%20%5B8.75e-07%2C%20%22m%22%5D%2C%20%22z%22%3A%20%5B0.0001%2C%20%22m%22%5D%7D%2C%20%22crossSectionScale%22%3A%2022.857142857142858%2C%20%22projectionScale%22%3A%2040000%2C%20%22selectedLayer%22%3A%20%7B%22visible%22%3A%20true%2C%20%22layer%22%3A%20%221145081396%20%2840_128_128%29%22%7D%2C%20%22layout%22%3A%20%224panel%22%2C%20%22layers%22%3A%20%5B%7B%22type%22%3A%20%22image%22%2C%20%22tab%22%3A%20%22rendering%22%2C%20%22shader%22%3A%20%22%5Cn%20%20%20%20%23uicontrol%20float%20red_min%20slider%28min%3D0.0%2C%20max%3D2688.0%29%5Cn%20%20%20%20%23uicontrol%20float%20red_max%20slider%28min%3D0.0%2C%20max%3D2688.0%29%5Cn%20%20%20%20%23uicontrol%20float%20green_min%20slider%28min%3D0.0%2C%20max%3D2608.0%29%5Cn%20%20%20%20%23uicontrol%20float%20green_max%20slider%28min%3D0.0%2C%20max%3D2608.0%29%5Cn%20%20%20%20%23uicontrol%20float%20blue_min%20slider%28min%3D0.0%2C%20max%3D8190.0%29%5Cn%20%20%20%20%23uicontrol%20float%20blue_max%20slider%28min%3D0.0%2C%20max%3D8190.0%29%5Cn%20%20%20%20%23uicontrol%20bool%20red_visible%20checkbox%28default%3Dtrue%29%3B%5Cn%20%20%20%20%23uicontrol%20bool%20green_visible%20checkbox%28default%3Dtrue%29%3B%5Cn%20%20%20%20%23uicontrol%20bool%20blue_visible%20checkbox%28default%3Dtrue%29%3B%5Cn%20%20%20%20%5Cn%20%20%20%20void%20main%28%29%20%7B%5Cn%20%20%20%20%20%20%20%20float%20r%3B%5Cn%20%20%20%20%20%20%20%20float%20r_scale%3Dred_max-red_min%3B%5Cn%20%20%20%20%20%20%20%20if%28%21red_visible%20%7C%7C%20%28r_scale%3C%3D0.0%29%20%29%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20r%3D0.0%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20else%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20r%3D%28float%28getDataValue%280%29.value%29-red_min%29/r_scale%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20if%28r%3E1.0%29r%3D1.0%3B%5Cn%5Cn%20%20%20%20%20%20%20%20%20float%20g%3B%5Cn%20%20%20%20%20%20%20%20%20float%20g_scale%3Dgreen_max-green_min%3B%5Cn%20%20%20%20%20%20%20%20%20if%28%21green_visible%20%7C%7C%20%28g_scale%3C%3D0.0%29%29%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20g%3D0.0%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20else%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20g%3D%28float%28getDataValue%281%29.value%29-green_min%29/g_scale%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20if%28g%3E1.0%29g%3D1.0%3B%5Cn%5Cn%20%20%20%20%20%20%20%20%20float%20b%3B%5Cn%20%20%20%20%20%20%20%20%20float%20b_scale%3Dblue_max-blue_min%3B%5Cn%20%20%20%20%20%20%20%20%20if%28%21blue_visible%20%7C%7C%20%28b_scale%3C%3D0.0%29%29%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20b%3D0.0%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20else%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20b%3D%28float%28getDataValue%282%29.value%29-blue_min%29/b_scale%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20if%28b%3E1.0%29b%3D1.0%3B%5Cn%5Cn%20%20%20%20%20%20%20%20%20emitRGB%28vec3%28r%2Cg%2Cb%29%29%3B%5Cn%20%20%20%20%20%7D%5Cn%20%20%20%20%20%22%2C%20%22shaderControls%22%3A%20%7B%22red_min%22%3A%200.0%2C%20%22red_max%22%3A%201344.0%2C%20%22green_min%22%3A%200.0%2C%20%22green_max%22%3A%201304.0%2C%20%22blue_min%22%3A%200.0%2C%20%22blue_max%22%3A%204095.0%7D%2C%20%22source%22%3A%20%7B%22url%22%3A%20%22zarr%3A//s3%3A//tissuecyte-ome-zarr-poc/40_128_128/1145081396%22%2C%20%22transform%22%3A%20%7B%22outputDimensions%22%3A%20%7B%22c%5E%22%3A%20%5B1%2C%20%22%22%5D%2C%20%22z%22%3A%20%5B0.0001%2C%20%22m%22%5D%2C%20%22y%22%3A%20%5B8.75e-07%2C%20%22m%22%5D%2C%20%22x%22%3A%20%5B8.75e-07%2C%20%22m%22%5D%7D%7D%7D%2C%20%22channelDimensions%22%3A%20%7B%22c%5E%22%3A%20%5B1%2C%20%22%22%5D%7D%2C%20%22name%22%3A%20%221145081396%20%2840_128_128%29%22%2C%20%22opacity%22%3A%201%7D%5D%7D',
},
{
- "function": "get_neuroglancer_url",
- "params": {
- "blue_max": 4095.0,
- "blue_min": 0.0,
- "cross_section_scale": 15.085714285714287,
- "green_max": 1304.0,
- "green_min": 0.0,
- "img_name": "1145081396 (40_128_128)",
- "layout": "xy",
- "red_max": 1344.0,
- "red_min": 0.0,
- "src_url": "zarr://s3://tissuecyte-ome-zarr-poc/40_128_128/1145081396",
- "x_mm": 0.000875,
- "y_mm": 0.000875,
- "z_mm": 0.1
- },
- "type": "Single image series; coronal projection",
- "url": "https://neuroglancer-demo.appspot.com/#!%7B%22dimensions%22%3A%20%7B%22x%22%3A%20%5B8.75e-07%2C%20%22m%22%5D%2C%20%22y%22%3A%20%5B8.75e-07%2C%20%22m%22%5D%2C%20%22z%22%3A%20%5B0.0001%2C%20%22m%22%5D%7D%2C%20%22crossSectionScale%22%3A%2015.085714285714287%2C%20%22projectionScale%22%3A%2040000%2C%20%22selectedLayer%22%3A%20%7B%22visible%22%3A%20true%2C%20%22layer%22%3A%20%221145081396%20%2840_128_128%29%22%7D%2C%20%22layout%22%3A%20%22xy%22%2C%20%22layers%22%3A%20%5B%7B%22type%22%3A%20%22image%22%2C%20%22tab%22%3A%20%22rendering%22%2C%20%22shader%22%3A%20%22%5Cn%20%20%20%20%23uicontrol%20float%20red_min%20slider%28min%3D0.0%2C%20max%3D2688.0%29%5Cn%20%20%20%20%23uicontrol%20float%20red_max%20slider%28min%3D0.0%2C%20max%3D2688.0%29%5Cn%20%20%20%20%23uicontrol%20float%20green_min%20slider%28min%3D0.0%2C%20max%3D2608.0%29%5Cn%20%20%20%20%23uicontrol%20float%20green_max%20slider%28min%3D0.0%2C%20max%3D2608.0%29%5Cn%20%20%20%20%23uicontrol%20float%20blue_min%20slider%28min%3D0.0%2C%20max%3D8190.0%29%5Cn%20%20%20%20%23uicontrol%20float%20blue_max%20slider%28min%3D0.0%2C%20max%3D8190.0%29%5Cn%20%20%20%20%23uicontrol%20bool%20red_visible%20checkbox%28default%3Dtrue%29%3B%5Cn%20%20%20%20%23uicontrol%20bool%20green_visible%20checkbox%28default%3Dtrue%29%3B%5Cn%20%20%20%20%23uicontrol%20bool%20blue_visible%20checkbox%28default%3Dtrue%29%3B%5Cn%20%20%20%20%5Cn%20%20%20%20void%20main%28%29%20%7B%5Cn%20%20%20%20%20%20%20%20float%20r%3B%5Cn%20%20%20%20%20%20%20%20float%20r_scale%3Dred_max-red_min%3B%5Cn%20%20%20%20%20%20%20%20if%28%21red_visible%20%7C%7C%20%28r_scale%3C%3D0.0%29%20%29%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20r%3D0.0%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20else%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20r%3D%28float%28getDataValue%280%29.value%29-red_min%29/r_scale%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20if%28r%3E1.0%29r%3D1.0%3B%5Cn%5Cn%20%20%20%20%20%20%20%20%20float%20g%3B%5Cn%20%20%20%20%20%20%20%20%20float%20g_scale%3Dgreen_max-green_min%3B%5Cn%20%20%20%20%20%20%20%20%20if%28%21green_visible%20%7C%7C%20%28g_scale%3C%3D0.0%29%29%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20g%3D0.0%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20else%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20g%3D%28float%28getDataValue%281%29.value%29-green_min%29/g_scale%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20if%28g%3E1.0%29g%3D1.0%3B%5Cn%5Cn%20%20%20%20%20%20%20%20%20float%20b%3B%5Cn%20%20%20%20%20%20%20%20%20float%20b_scale%3Dblue_max-blue_min%3B%5Cn%20%20%20%20%20%20%20%20%20if%28%21blue_visible%20%7C%7C%20%28b_scale%3C%3D0.0%29%29%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20b%3D0.0%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20else%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20b%3D%28float%28getDataValue%282%29.value%29-blue_min%29/b_scale%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20if%28b%3E1.0%29b%3D1.0%3B%5Cn%5Cn%20%20%20%20%20%20%20%20%20emitRGB%28vec3%28r%2Cg%2Cb%29%29%3B%5Cn%20%20%20%20%20%7D%5Cn%20%20%20%20%20%22%2C%20%22shaderControls%22%3A%20%7B%22red_min%22%3A%200.0%2C%20%22red_max%22%3A%201344.0%2C%20%22green_min%22%3A%200.0%2C%20%22green_max%22%3A%201304.0%2C%20%22blue_min%22%3A%200.0%2C%20%22blue_max%22%3A%204095.0%7D%2C%20%22source%22%3A%20%7B%22url%22%3A%20%22zarr%3A//s3%3A//tissuecyte-ome-zarr-poc/40_128_128/1145081396%22%2C%20%22transform%22%3A%20%7B%22outputDimensions%22%3A%20%7B%22c%5E%22%3A%20%5B1%2C%20%22%22%5D%2C%20%22z%22%3A%20%5B0.0001%2C%20%22m%22%5D%2C%20%22y%22%3A%20%5B8.75e-07%2C%20%22m%22%5D%2C%20%22x%22%3A%20%5B8.75e-07%2C%20%22m%22%5D%7D%7D%7D%2C%20%22channelDimensions%22%3A%20%7B%22c%5E%22%3A%20%5B1%2C%20%22%22%5D%7D%2C%20%22name%22%3A%20%221145081396%20%2840_128_128%29%22%2C%20%22opacity%22%3A%201%7D%5D%7D"
+ function: 'get_neuroglancer_url',
+ params: {
+ blue_max: 4095.0,
+ blue_min: 0.0,
+ cross_section_scale: 15.085714285714287,
+ green_max: 1304.0,
+ green_min: 0.0,
+ img_name: '1145081396 (40_128_128)',
+ layout: 'xy',
+ red_max: 1344.0,
+ red_min: 0.0,
+ src_url: 'zarr://s3://tissuecyte-ome-zarr-poc/40_128_128/1145081396',
+ x_mm: 0.000875,
+ y_mm: 0.000875,
+ z_mm: 0.1,
+ },
+ type: 'Single image series; coronal projection',
+ url: 'https://neuroglancer-demo.appspot.com/#!%7B%22dimensions%22%3A%20%7B%22x%22%3A%20%5B8.75e-07%2C%20%22m%22%5D%2C%20%22y%22%3A%20%5B8.75e-07%2C%20%22m%22%5D%2C%20%22z%22%3A%20%5B0.0001%2C%20%22m%22%5D%7D%2C%20%22crossSectionScale%22%3A%2015.085714285714287%2C%20%22projectionScale%22%3A%2040000%2C%20%22selectedLayer%22%3A%20%7B%22visible%22%3A%20true%2C%20%22layer%22%3A%20%221145081396%20%2840_128_128%29%22%7D%2C%20%22layout%22%3A%20%22xy%22%2C%20%22layers%22%3A%20%5B%7B%22type%22%3A%20%22image%22%2C%20%22tab%22%3A%20%22rendering%22%2C%20%22shader%22%3A%20%22%5Cn%20%20%20%20%23uicontrol%20float%20red_min%20slider%28min%3D0.0%2C%20max%3D2688.0%29%5Cn%20%20%20%20%23uicontrol%20float%20red_max%20slider%28min%3D0.0%2C%20max%3D2688.0%29%5Cn%20%20%20%20%23uicontrol%20float%20green_min%20slider%28min%3D0.0%2C%20max%3D2608.0%29%5Cn%20%20%20%20%23uicontrol%20float%20green_max%20slider%28min%3D0.0%2C%20max%3D2608.0%29%5Cn%20%20%20%20%23uicontrol%20float%20blue_min%20slider%28min%3D0.0%2C%20max%3D8190.0%29%5Cn%20%20%20%20%23uicontrol%20float%20blue_max%20slider%28min%3D0.0%2C%20max%3D8190.0%29%5Cn%20%20%20%20%23uicontrol%20bool%20red_visible%20checkbox%28default%3Dtrue%29%3B%5Cn%20%20%20%20%23uicontrol%20bool%20green_visible%20checkbox%28default%3Dtrue%29%3B%5Cn%20%20%20%20%23uicontrol%20bool%20blue_visible%20checkbox%28default%3Dtrue%29%3B%5Cn%20%20%20%20%5Cn%20%20%20%20void%20main%28%29%20%7B%5Cn%20%20%20%20%20%20%20%20float%20r%3B%5Cn%20%20%20%20%20%20%20%20float%20r_scale%3Dred_max-red_min%3B%5Cn%20%20%20%20%20%20%20%20if%28%21red_visible%20%7C%7C%20%28r_scale%3C%3D0.0%29%20%29%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20r%3D0.0%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20else%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20r%3D%28float%28getDataValue%280%29.value%29-red_min%29/r_scale%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20if%28r%3E1.0%29r%3D1.0%3B%5Cn%5Cn%20%20%20%20%20%20%20%20%20float%20g%3B%5Cn%20%20%20%20%20%20%20%20%20float%20g_scale%3Dgreen_max-green_min%3B%5Cn%20%20%20%20%20%20%20%20%20if%28%21green_visible%20%7C%7C%20%28g_scale%3C%3D0.0%29%29%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20g%3D0.0%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20else%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20g%3D%28float%28getDataValue%281%29.value%29-green_min%29/g_scale%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20if%28g%3E1.0%29g%3D1.0%3B%5Cn%5Cn%20%20%20%20%20%20%20%20%20float%20b%3B%5Cn%20%20%20%20%20%20%20%20%20float%20b_scale%3Dblue_max-blue_min%3B%5Cn%20%20%20%20%20%20%20%20%20if%28%21blue_visible%20%7C%7C%20%28b_scale%3C%3D0.0%29%29%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20b%3D0.0%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20else%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20b%3D%28float%28getDataValue%282%29.value%29-blue_min%29/b_scale%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20if%28b%3E1.0%29b%3D1.0%3B%5Cn%5Cn%20%20%20%20%20%20%20%20%20emitRGB%28vec3%28r%2Cg%2Cb%29%29%3B%5Cn%20%20%20%20%20%7D%5Cn%20%20%20%20%20%22%2C%20%22shaderControls%22%3A%20%7B%22red_min%22%3A%200.0%2C%20%22red_max%22%3A%201344.0%2C%20%22green_min%22%3A%200.0%2C%20%22green_max%22%3A%201304.0%2C%20%22blue_min%22%3A%200.0%2C%20%22blue_max%22%3A%204095.0%7D%2C%20%22source%22%3A%20%7B%22url%22%3A%20%22zarr%3A//s3%3A//tissuecyte-ome-zarr-poc/40_128_128/1145081396%22%2C%20%22transform%22%3A%20%7B%22outputDimensions%22%3A%20%7B%22c%5E%22%3A%20%5B1%2C%20%22%22%5D%2C%20%22z%22%3A%20%5B0.0001%2C%20%22m%22%5D%2C%20%22y%22%3A%20%5B8.75e-07%2C%20%22m%22%5D%2C%20%22x%22%3A%20%5B8.75e-07%2C%20%22m%22%5D%7D%7D%7D%2C%20%22channelDimensions%22%3A%20%7B%22c%5E%22%3A%20%5B1%2C%20%22%22%5D%7D%2C%20%22name%22%3A%20%221145081396%20%2840_128_128%29%22%2C%20%22opacity%22%3A%201%7D%5D%7D',
},
{
- "function": "get_contact_sheet_url",
- "params": {
- "blue_max": 4095.0,
- "blue_min": 0.0,
- "cross_section_scale": 230.4,
- "green_max": 1304.0,
- "green_min": 0.0,
- "img_name": "1145081396 (40_128_128)",
- "ome_zarr_shape": [
- 3,
- 142,
- 11998,
- 15998
- ],
- "red_max": 1344.0,
- "red_min": 0.0,
- "src_url": "zarr://s3://tissuecyte-ome-zarr-poc/40_128_128/1145081396",
- "x_mm": 0.000875,
- "y_mm": 0.000875,
- "z_mm": 0.1
- },
- "type": "Single image series; contact sheet",
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+ function: 'get_contact_sheet_url',
+ params: {
+ blue_max: 4095.0,
+ blue_min: 0.0,
+ cross_section_scale: 230.4,
+ green_max: 1304.0,
+ green_min: 0.0,
+ img_name: '1145081396 (40_128_128)',
+ ome_zarr_shape: [3, 142, 11998, 15998],
+ red_max: 1344.0,
+ red_min: 0.0,
+ src_url: 'zarr://s3://tissuecyte-ome-zarr-poc/40_128_128/1145081396',
+ x_mm: 0.000875,
+ y_mm: 0.000875,
+ z_mm: 0.1,
+ },
+ type: 'Single image series; contact sheet',
+ url: 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},
{
- "function": "get_neuroglancer_url",
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- },
- "type": "Single image series; all three planes",
- "url": "https://neuroglancer-demo.appspot.com/#!%7B%22dimensions%22%3A%20%7B%22x%22%3A%20%5B3.5e-07%2C%20%22m%22%5D%2C%20%22y%22%3A%20%5B3.5e-07%2C%20%22m%22%5D%2C%20%22z%22%3A%20%5B0.0001%2C%20%22m%22%5D%7D%2C%20%22crossSectionScale%22%3A%2057.142857142857146%2C%20%22projectionScale%22%3A%2040000%2C%20%22selectedLayer%22%3A%20%7B%22visible%22%3A%20true%2C%20%22layer%22%3A%20%221182837942%20%2840_128_128%29%22%7D%2C%20%22layout%22%3A%20%224panel%22%2C%20%22layers%22%3A%20%5B%7B%22type%22%3A%20%22image%22%2C%20%22tab%22%3A%20%22rendering%22%2C%20%22shader%22%3A%20%22%5Cn%20%20%20%20%23uicontrol%20float%20red_min%20slider%28min%3D0.0%2C%20max%3D1728.0%29%5Cn%20%20%20%20%23uicontrol%20float%20red_max%20slider%28min%3D0.0%2C%20max%3D1728.0%29%5Cn%20%20%20%20%23uicontrol%20float%20green_min%20slider%28min%3D0.0%2C%20max%3D8090.0%29%5Cn%20%20%20%20%23uicontrol%20float%20green_max%20slider%28min%3D0.0%2C%20max%3D8090.0%29%5Cn%20%20%20%20%23uicontrol%20float%20blue_min%20slider%28min%3D0.0%2C%20max%3D8190.0%29%5Cn%20%20%20%20%23uicontrol%20float%20blue_max%20slider%28min%3D0.0%2C%20max%3D8190.0%29%5Cn%20%20%20%20%23uicontrol%20bool%20red_visible%20checkbox%28default%3Dtrue%29%3B%5Cn%20%20%20%20%23uicontrol%20bool%20green_visible%20checkbox%28default%3Dtrue%29%3B%5Cn%20%20%20%20%23uicontrol%20bool%20blue_visible%20checkbox%28default%3Dtrue%29%3B%5Cn%20%20%20%20%5Cn%20%20%20%20void%20main%28%29%20%7B%5Cn%20%20%20%20%20%20%20%20float%20r%3B%5Cn%20%20%20%20%20%20%20%20float%20r_scale%3Dred_max-red_min%3B%5Cn%20%20%20%20%20%20%20%20if%28%21red_visible%20%7C%7C%20%28r_scale%3C%3D0.0%29%20%29%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20r%3D0.0%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20else%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20r%3D%28float%28getDataValue%280%29.value%29-red_min%29/r_scale%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20if%28r%3E1.0%29r%3D1.0%3B%5Cn%5Cn%20%20%20%20%20%20%20%20%20float%20g%3B%5Cn%20%20%20%20%20%20%20%20%20float%20g_scale%3Dgreen_max-green_min%3B%5Cn%20%20%20%20%20%20%20%20%20if%28%21green_visible%20%7C%7C%20%28g_scale%3C%3D0.0%29%29%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20g%3D0.0%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20else%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20g%3D%28float%28getDataValue%281%29.value%29-green_min%29/g_scale%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20if%28g%3E1.0%29g%3D1.0%3B%5Cn%5Cn%20%20%20%20%20%20%20%20%20float%20b%3B%5Cn%20%20%20%20%20%20%20%20%20float%20b_scale%3Dblue_max-blue_min%3B%5Cn%20%20%20%20%20%20%20%20%20if%28%21blue_visible%20%7C%7C%20%28b_scale%3C%3D0.0%29%29%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20b%3D0.0%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20else%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20b%3D%28float%28getDataValue%282%29.value%29-blue_min%29/b_scale%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20if%28b%3E1.0%29b%3D1.0%3B%5Cn%5Cn%20%20%20%20%20%20%20%20%20emitRGB%28vec3%28r%2Cg%2Cb%29%29%3B%5Cn%20%20%20%20%20%7D%5Cn%20%20%20%20%20%22%2C%20%22shaderControls%22%3A%20%7B%22red_min%22%3A%200.0%2C%20%22red_max%22%3A%20864.0%2C%20%22green_min%22%3A%200.0%2C%20%22green_max%22%3A%204045.0%2C%20%22blue_min%22%3A%200.0%2C%20%22blue_max%22%3A%204095.0%7D%2C%20%22source%22%3A%20%7B%22url%22%3A%20%22zarr%3A//s3%3A//tissuecyte-ome-zarr-poc/40_128_128/1182837942%22%2C%20%22transform%22%3A%20%7B%22outputDimensions%22%3A%20%7B%22c%5E%22%3A%20%5B1%2C%20%22%22%5D%2C%20%22z%22%3A%20%5B0.0001%2C%20%22m%22%5D%2C%20%22y%22%3A%20%5B3.5e-07%2C%20%22m%22%5D%2C%20%22x%22%3A%20%5B3.5e-07%2C%20%22m%22%5D%7D%7D%7D%2C%20%22channelDimensions%22%3A%20%7B%22c%5E%22%3A%20%5B1%2C%20%22%22%5D%7D%2C%20%22name%22%3A%20%221182837942%20%2840_128_128%29%22%2C%20%22opacity%22%3A%201%7D%5D%7D"
+ function: 'get_neuroglancer_url',
+ params: {
+ blue_max: 4095.0,
+ blue_min: 0.0,
+ cross_section_scale: 57.142857142857146,
+ green_max: 4045.0,
+ green_min: 0.0,
+ img_name: '1182837942 (40_128_128)',
+ layout: '4panel',
+ red_max: 864.0,
+ red_min: 0.0,
+ src_url: 'zarr://s3://tissuecyte-ome-zarr-poc/40_128_128/1182837942',
+ x_mm: 0.00035,
+ y_mm: 0.00035,
+ z_mm: 0.1,
+ },
+ type: 'Single image series; all three planes',
+ url: 'https://neuroglancer-demo.appspot.com/#!%7B%22dimensions%22%3A%20%7B%22x%22%3A%20%5B3.5e-07%2C%20%22m%22%5D%2C%20%22y%22%3A%20%5B3.5e-07%2C%20%22m%22%5D%2C%20%22z%22%3A%20%5B0.0001%2C%20%22m%22%5D%7D%2C%20%22crossSectionScale%22%3A%2057.142857142857146%2C%20%22projectionScale%22%3A%2040000%2C%20%22selectedLayer%22%3A%20%7B%22visible%22%3A%20true%2C%20%22layer%22%3A%20%221182837942%20%2840_128_128%29%22%7D%2C%20%22layout%22%3A%20%224panel%22%2C%20%22layers%22%3A%20%5B%7B%22type%22%3A%20%22image%22%2C%20%22tab%22%3A%20%22rendering%22%2C%20%22shader%22%3A%20%22%5Cn%20%20%20%20%23uicontrol%20float%20red_min%20slider%28min%3D0.0%2C%20max%3D1728.0%29%5Cn%20%20%20%20%23uicontrol%20float%20red_max%20slider%28min%3D0.0%2C%20max%3D1728.0%29%5Cn%20%20%20%20%23uicontrol%20float%20green_min%20slider%28min%3D0.0%2C%20max%3D8090.0%29%5Cn%20%20%20%20%23uicontrol%20float%20green_max%20slider%28min%3D0.0%2C%20max%3D8090.0%29%5Cn%20%20%20%20%23uicontrol%20float%20blue_min%20slider%28min%3D0.0%2C%20max%3D8190.0%29%5Cn%20%20%20%20%23uicontrol%20float%20blue_max%20slider%28min%3D0.0%2C%20max%3D8190.0%29%5Cn%20%20%20%20%23uicontrol%20bool%20red_visible%20checkbox%28default%3Dtrue%29%3B%5Cn%20%20%20%20%23uicontrol%20bool%20green_visible%20checkbox%28default%3Dtrue%29%3B%5Cn%20%20%20%20%23uicontrol%20bool%20blue_visible%20checkbox%28default%3Dtrue%29%3B%5Cn%20%20%20%20%5Cn%20%20%20%20void%20main%28%29%20%7B%5Cn%20%20%20%20%20%20%20%20float%20r%3B%5Cn%20%20%20%20%20%20%20%20float%20r_scale%3Dred_max-red_min%3B%5Cn%20%20%20%20%20%20%20%20if%28%21red_visible%20%7C%7C%20%28r_scale%3C%3D0.0%29%20%29%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20r%3D0.0%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20else%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20r%3D%28float%28getDataValue%280%29.value%29-red_min%29/r_scale%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20if%28r%3E1.0%29r%3D1.0%3B%5Cn%5Cn%20%20%20%20%20%20%20%20%20float%20g%3B%5Cn%20%20%20%20%20%20%20%20%20float%20g_scale%3Dgreen_max-green_min%3B%5Cn%20%20%20%20%20%20%20%20%20if%28%21green_visible%20%7C%7C%20%28g_scale%3C%3D0.0%29%29%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20g%3D0.0%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20else%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20g%3D%28float%28getDataValue%281%29.value%29-green_min%29/g_scale%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20if%28g%3E1.0%29g%3D1.0%3B%5Cn%5Cn%20%20%20%20%20%20%20%20%20float%20b%3B%5Cn%20%20%20%20%20%20%20%20%20float%20b_scale%3Dblue_max-blue_min%3B%5Cn%20%20%20%20%20%20%20%20%20if%28%21blue_visible%20%7C%7C%20%28b_scale%3C%3D0.0%29%29%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20b%3D0.0%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20else%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20b%3D%28float%28getDataValue%282%29.value%29-blue_min%29/b_scale%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20if%28b%3E1.0%29b%3D1.0%3B%5Cn%5Cn%20%20%20%20%20%20%20%20%20emitRGB%28vec3%28r%2Cg%2Cb%29%29%3B%5Cn%20%20%20%20%20%7D%5Cn%20%20%20%20%20%22%2C%20%22shaderControls%22%3A%20%7B%22red_min%22%3A%200.0%2C%20%22red_max%22%3A%20864.0%2C%20%22green_min%22%3A%200.0%2C%20%22green_max%22%3A%204045.0%2C%20%22blue_min%22%3A%200.0%2C%20%22blue_max%22%3A%204095.0%7D%2C%20%22source%22%3A%20%7B%22url%22%3A%20%22zarr%3A//s3%3A//tissuecyte-ome-zarr-poc/40_128_128/1182837942%22%2C%20%22transform%22%3A%20%7B%22outputDimensions%22%3A%20%7B%22c%5E%22%3A%20%5B1%2C%20%22%22%5D%2C%20%22z%22%3A%20%5B0.0001%2C%20%22m%22%5D%2C%20%22y%22%3A%20%5B3.5e-07%2C%20%22m%22%5D%2C%20%22x%22%3A%20%5B3.5e-07%2C%20%22m%22%5D%7D%7D%7D%2C%20%22channelDimensions%22%3A%20%7B%22c%5E%22%3A%20%5B1%2C%20%22%22%5D%7D%2C%20%22name%22%3A%20%221182837942%20%2840_128_128%29%22%2C%20%22opacity%22%3A%201%7D%5D%7D',
},
{
- "function": "get_neuroglancer_url",
- "params": {
- "blue_max": 4095.0,
- "blue_min": 0.0,
- "cross_section_scale": 37.714285714285715,
- "green_max": 4045.0,
- "green_min": 0.0,
- "img_name": "1182837942 (40_128_128)",
- "layout": "xy",
- "red_max": 864.0,
- "red_min": 0.0,
- "src_url": "zarr://s3://tissuecyte-ome-zarr-poc/40_128_128/1182837942",
- "x_mm": 0.00035,
- "y_mm": 0.00035,
- "z_mm": 0.1
- },
- "type": "Single image series; coronal projection",
- "url": "https://neuroglancer-demo.appspot.com/#!%7B%22dimensions%22%3A%20%7B%22x%22%3A%20%5B3.5e-07%2C%20%22m%22%5D%2C%20%22y%22%3A%20%5B3.5e-07%2C%20%22m%22%5D%2C%20%22z%22%3A%20%5B0.0001%2C%20%22m%22%5D%7D%2C%20%22crossSectionScale%22%3A%2037.714285714285715%2C%20%22projectionScale%22%3A%2040000%2C%20%22selectedLayer%22%3A%20%7B%22visible%22%3A%20true%2C%20%22layer%22%3A%20%221182837942%20%2840_128_128%29%22%7D%2C%20%22layout%22%3A%20%22xy%22%2C%20%22layers%22%3A%20%5B%7B%22type%22%3A%20%22image%22%2C%20%22tab%22%3A%20%22rendering%22%2C%20%22shader%22%3A%20%22%5Cn%20%20%20%20%23uicontrol%20float%20red_min%20slider%28min%3D0.0%2C%20max%3D1728.0%29%5Cn%20%20%20%20%23uicontrol%20float%20red_max%20slider%28min%3D0.0%2C%20max%3D1728.0%29%5Cn%20%20%20%20%23uicontrol%20float%20green_min%20slider%28min%3D0.0%2C%20max%3D8090.0%29%5Cn%20%20%20%20%23uicontrol%20float%20green_max%20slider%28min%3D0.0%2C%20max%3D8090.0%29%5Cn%20%20%20%20%23uicontrol%20float%20blue_min%20slider%28min%3D0.0%2C%20max%3D8190.0%29%5Cn%20%20%20%20%23uicontrol%20float%20blue_max%20slider%28min%3D0.0%2C%20max%3D8190.0%29%5Cn%20%20%20%20%23uicontrol%20bool%20red_visible%20checkbox%28default%3Dtrue%29%3B%5Cn%20%20%20%20%23uicontrol%20bool%20green_visible%20checkbox%28default%3Dtrue%29%3B%5Cn%20%20%20%20%23uicontrol%20bool%20blue_visible%20checkbox%28default%3Dtrue%29%3B%5Cn%20%20%20%20%5Cn%20%20%20%20void%20main%28%29%20%7B%5Cn%20%20%20%20%20%20%20%20float%20r%3B%5Cn%20%20%20%20%20%20%20%20float%20r_scale%3Dred_max-red_min%3B%5Cn%20%20%20%20%20%20%20%20if%28%21red_visible%20%7C%7C%20%28r_scale%3C%3D0.0%29%20%29%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20r%3D0.0%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20else%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20r%3D%28float%28getDataValue%280%29.value%29-red_min%29/r_scale%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20if%28r%3E1.0%29r%3D1.0%3B%5Cn%5Cn%20%20%20%20%20%20%20%20%20float%20g%3B%5Cn%20%20%20%20%20%20%20%20%20float%20g_scale%3Dgreen_max-green_min%3B%5Cn%20%20%20%20%20%20%20%20%20if%28%21green_visible%20%7C%7C%20%28g_scale%3C%3D0.0%29%29%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20g%3D0.0%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20else%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20g%3D%28float%28getDataValue%281%29.value%29-green_min%29/g_scale%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20if%28g%3E1.0%29g%3D1.0%3B%5Cn%5Cn%20%20%20%20%20%20%20%20%20float%20b%3B%5Cn%20%20%20%20%20%20%20%20%20float%20b_scale%3Dblue_max-blue_min%3B%5Cn%20%20%20%20%20%20%20%20%20if%28%21blue_visible%20%7C%7C%20%28b_scale%3C%3D0.0%29%29%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20b%3D0.0%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20else%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20b%3D%28float%28getDataValue%282%29.value%29-blue_min%29/b_scale%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20if%28b%3E1.0%29b%3D1.0%3B%5Cn%5Cn%20%20%20%20%20%20%20%20%20emitRGB%28vec3%28r%2Cg%2Cb%29%29%3B%5Cn%20%20%20%20%20%7D%5Cn%20%20%20%20%20%22%2C%20%22shaderControls%22%3A%20%7B%22red_min%22%3A%200.0%2C%20%22red_max%22%3A%20864.0%2C%20%22green_min%22%3A%200.0%2C%20%22green_max%22%3A%204045.0%2C%20%22blue_min%22%3A%200.0%2C%20%22blue_max%22%3A%204095.0%7D%2C%20%22source%22%3A%20%7B%22url%22%3A%20%22zarr%3A//s3%3A//tissuecyte-ome-zarr-poc/40_128_128/1182837942%22%2C%20%22transform%22%3A%20%7B%22outputDimensions%22%3A%20%7B%22c%5E%22%3A%20%5B1%2C%20%22%22%5D%2C%20%22z%22%3A%20%5B0.0001%2C%20%22m%22%5D%2C%20%22y%22%3A%20%5B3.5e-07%2C%20%22m%22%5D%2C%20%22x%22%3A%20%5B3.5e-07%2C%20%22m%22%5D%7D%7D%7D%2C%20%22channelDimensions%22%3A%20%7B%22c%5E%22%3A%20%5B1%2C%20%22%22%5D%7D%2C%20%22name%22%3A%20%221182837942%20%2840_128_128%29%22%2C%20%22opacity%22%3A%201%7D%5D%7D"
+ function: 'get_neuroglancer_url',
+ params: {
+ blue_max: 4095.0,
+ blue_min: 0.0,
+ cross_section_scale: 37.714285714285715,
+ green_max: 4045.0,
+ green_min: 0.0,
+ img_name: '1182837942 (40_128_128)',
+ layout: 'xy',
+ red_max: 864.0,
+ red_min: 0.0,
+ src_url: 'zarr://s3://tissuecyte-ome-zarr-poc/40_128_128/1182837942',
+ x_mm: 0.00035,
+ y_mm: 0.00035,
+ z_mm: 0.1,
+ },
+ type: 'Single image series; coronal projection',
+ url: 'https://neuroglancer-demo.appspot.com/#!%7B%22dimensions%22%3A%20%7B%22x%22%3A%20%5B3.5e-07%2C%20%22m%22%5D%2C%20%22y%22%3A%20%5B3.5e-07%2C%20%22m%22%5D%2C%20%22z%22%3A%20%5B0.0001%2C%20%22m%22%5D%7D%2C%20%22crossSectionScale%22%3A%2037.714285714285715%2C%20%22projectionScale%22%3A%2040000%2C%20%22selectedLayer%22%3A%20%7B%22visible%22%3A%20true%2C%20%22layer%22%3A%20%221182837942%20%2840_128_128%29%22%7D%2C%20%22layout%22%3A%20%22xy%22%2C%20%22layers%22%3A%20%5B%7B%22type%22%3A%20%22image%22%2C%20%22tab%22%3A%20%22rendering%22%2C%20%22shader%22%3A%20%22%5Cn%20%20%20%20%23uicontrol%20float%20red_min%20slider%28min%3D0.0%2C%20max%3D1728.0%29%5Cn%20%20%20%20%23uicontrol%20float%20red_max%20slider%28min%3D0.0%2C%20max%3D1728.0%29%5Cn%20%20%20%20%23uicontrol%20float%20green_min%20slider%28min%3D0.0%2C%20max%3D8090.0%29%5Cn%20%20%20%20%23uicontrol%20float%20green_max%20slider%28min%3D0.0%2C%20max%3D8090.0%29%5Cn%20%20%20%20%23uicontrol%20float%20blue_min%20slider%28min%3D0.0%2C%20max%3D8190.0%29%5Cn%20%20%20%20%23uicontrol%20float%20blue_max%20slider%28min%3D0.0%2C%20max%3D8190.0%29%5Cn%20%20%20%20%23uicontrol%20bool%20red_visible%20checkbox%28default%3Dtrue%29%3B%5Cn%20%20%20%20%23uicontrol%20bool%20green_visible%20checkbox%28default%3Dtrue%29%3B%5Cn%20%20%20%20%23uicontrol%20bool%20blue_visible%20checkbox%28default%3Dtrue%29%3B%5Cn%20%20%20%20%5Cn%20%20%20%20void%20main%28%29%20%7B%5Cn%20%20%20%20%20%20%20%20float%20r%3B%5Cn%20%20%20%20%20%20%20%20float%20r_scale%3Dred_max-red_min%3B%5Cn%20%20%20%20%20%20%20%20if%28%21red_visible%20%7C%7C%20%28r_scale%3C%3D0.0%29%20%29%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20r%3D0.0%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20else%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20r%3D%28float%28getDataValue%280%29.value%29-red_min%29/r_scale%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20if%28r%3E1.0%29r%3D1.0%3B%5Cn%5Cn%20%20%20%20%20%20%20%20%20float%20g%3B%5Cn%20%20%20%20%20%20%20%20%20float%20g_scale%3Dgreen_max-green_min%3B%5Cn%20%20%20%20%20%20%20%20%20if%28%21green_visible%20%7C%7C%20%28g_scale%3C%3D0.0%29%29%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20g%3D0.0%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20else%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20g%3D%28float%28getDataValue%281%29.value%29-green_min%29/g_scale%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20if%28g%3E1.0%29g%3D1.0%3B%5Cn%5Cn%20%20%20%20%20%20%20%20%20float%20b%3B%5Cn%20%20%20%20%20%20%20%20%20float%20b_scale%3Dblue_max-blue_min%3B%5Cn%20%20%20%20%20%20%20%20%20if%28%21blue_visible%20%7C%7C%20%28b_scale%3C%3D0.0%29%29%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20b%3D0.0%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20else%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20b%3D%28float%28getDataValue%282%29.value%29-blue_min%29/b_scale%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20if%28b%3E1.0%29b%3D1.0%3B%5Cn%5Cn%20%20%20%20%20%20%20%20%20emitRGB%28vec3%28r%2Cg%2Cb%29%29%3B%5Cn%20%20%20%20%20%7D%5Cn%20%20%20%20%20%22%2C%20%22shaderControls%22%3A%20%7B%22red_min%22%3A%200.0%2C%20%22red_max%22%3A%20864.0%2C%20%22green_min%22%3A%200.0%2C%20%22green_max%22%3A%204045.0%2C%20%22blue_min%22%3A%200.0%2C%20%22blue_max%22%3A%204095.0%7D%2C%20%22source%22%3A%20%7B%22url%22%3A%20%22zarr%3A//s3%3A//tissuecyte-ome-zarr-poc/40_128_128/1182837942%22%2C%20%22transform%22%3A%20%7B%22outputDimensions%22%3A%20%7B%22c%5E%22%3A%20%5B1%2C%20%22%22%5D%2C%20%22z%22%3A%20%5B0.0001%2C%20%22m%22%5D%2C%20%22y%22%3A%20%5B3.5e-07%2C%20%22m%22%5D%2C%20%22x%22%3A%20%5B3.5e-07%2C%20%22m%22%5D%7D%7D%7D%2C%20%22channelDimensions%22%3A%20%7B%22c%5E%22%3A%20%5B1%2C%20%22%22%5D%7D%2C%20%22name%22%3A%20%221182837942%20%2840_128_128%29%22%2C%20%22opacity%22%3A%201%7D%5D%7D',
},
{
- "function": "get_contact_sheet_url",
- "params": {
- "blue_max": 4095.0,
- "blue_min": 0.0,
- "cross_section_scale": 576.0,
- "green_max": 4045.0,
- "green_min": 0.0,
- "img_name": "1182837942 (40_128_128)",
- "ome_zarr_shape": [
- 3,
- 142,
- 29998,
- 39998
- ],
- "red_max": 864.0,
- "red_min": 0.0,
- "src_url": "zarr://s3://tissuecyte-ome-zarr-poc/40_128_128/1182837942",
- "x_mm": 0.00035,
- "y_mm": 0.00035,
- "z_mm": 0.1
- },
- "type": "Single image series; contact sheet",
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+ function: 'get_contact_sheet_url',
+ params: {
+ blue_max: 4095.0,
+ blue_min: 0.0,
+ cross_section_scale: 576.0,
+ green_max: 4045.0,
+ green_min: 0.0,
+ img_name: '1182837942 (40_128_128)',
+ ome_zarr_shape: [3, 142, 29998, 39998],
+ red_max: 864.0,
+ red_min: 0.0,
+ src_url: 'zarr://s3://tissuecyte-ome-zarr-poc/40_128_128/1182837942',
+ x_mm: 0.00035,
+ y_mm: 0.00035,
+ z_mm: 0.1,
+ },
+ type: 'Single image series; contact sheet',
+ url: 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},
{
- "function": "get_neuroglancer_url",
- "params": {
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- "cross_section_scale": 57.142857142857146,
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- "x_mm": 0.00035,
- "y_mm": 0.00035,
- "z_mm": 0.1
- },
- "type": "Single image series; all three planes",
- "url": "https://neuroglancer-demo.appspot.com/#!%7B%22dimensions%22%3A%20%7B%22x%22%3A%20%5B3.5e-07%2C%20%22m%22%5D%2C%20%22y%22%3A%20%5B3.5e-07%2C%20%22m%22%5D%2C%20%22z%22%3A%20%5B0.0001%2C%20%22m%22%5D%7D%2C%20%22crossSectionScale%22%3A%2057.142857142857146%2C%20%22projectionScale%22%3A%2040000%2C%20%22selectedLayer%22%3A%20%7B%22visible%22%3A%20true%2C%20%22layer%22%3A%20%221240649363%20%2840_128_128%29%22%7D%2C%20%22layout%22%3A%20%224panel%22%2C%20%22layers%22%3A%20%5B%7B%22type%22%3A%20%22image%22%2C%20%22tab%22%3A%20%22rendering%22%2C%20%22shader%22%3A%20%22%5Cn%20%20%20%20%23uicontrol%20float%20red_min%20slider%28min%3D0.0%2C%20max%3D2712.0%29%5Cn%20%20%20%20%23uicontrol%20float%20red_max%20slider%28min%3D0.0%2C%20max%3D2712.0%29%5Cn%20%20%20%20%23uicontrol%20float%20green_min%20slider%28min%3D0.0%2C%20max%3D6026.0%29%5Cn%20%20%20%20%23uicontrol%20float%20green_max%20slider%28min%3D0.0%2C%20max%3D6026.0%29%5Cn%20%20%20%20%23uicontrol%20float%20blue_min%20slider%28min%3D0.0%2C%20max%3D8190.0%29%5Cn%20%20%20%20%23uicontrol%20float%20blue_max%20slider%28min%3D0.0%2C%20max%3D8190.0%29%5Cn%20%20%20%20%23uicontrol%20bool%20red_visible%20checkbox%28default%3Dtrue%29%3B%5Cn%20%20%20%20%23uicontrol%20bool%20green_visible%20checkbox%28default%3Dtrue%29%3B%5Cn%20%20%20%20%23uicontrol%20bool%20blue_visible%20checkbox%28default%3Dtrue%29%3B%5Cn%20%20%20%20%5Cn%20%20%20%20void%20main%28%29%20%7B%5Cn%20%20%20%20%20%20%20%20float%20r%3B%5Cn%20%20%20%20%20%20%20%20float%20r_scale%3Dred_max-red_min%3B%5Cn%20%20%20%20%20%20%20%20if%28%21red_visible%20%7C%7C%20%28r_scale%3C%3D0.0%29%20%29%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20r%3D0.0%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20else%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20r%3D%28float%28getDataValue%280%29.value%29-red_min%29/r_scale%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20if%28r%3E1.0%29r%3D1.0%3B%5Cn%5Cn%20%20%20%20%20%20%20%20%20float%20g%3B%5Cn%20%20%20%20%20%20%20%20%20float%20g_scale%3Dgreen_max-green_min%3B%5Cn%20%20%20%20%20%20%20%20%20if%28%21green_visible%20%7C%7C%20%28g_scale%3C%3D0.0%29%29%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20g%3D0.0%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20else%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20g%3D%28float%28getDataValue%281%29.value%29-green_min%29/g_scale%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20if%28g%3E1.0%29g%3D1.0%3B%5Cn%5Cn%20%20%20%20%20%20%20%20%20float%20b%3B%5Cn%20%20%20%20%20%20%20%20%20float%20b_scale%3Dblue_max-blue_min%3B%5Cn%20%20%20%20%20%20%20%20%20if%28%21blue_visible%20%7C%7C%20%28b_scale%3C%3D0.0%29%29%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20b%3D0.0%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20else%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20b%3D%28float%28getDataValue%282%29.value%29-blue_min%29/b_scale%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20if%28b%3E1.0%29b%3D1.0%3B%5Cn%5Cn%20%20%20%20%20%20%20%20%20emitRGB%28vec3%28r%2Cg%2Cb%29%29%3B%5Cn%20%20%20%20%20%7D%5Cn%20%20%20%20%20%22%2C%20%22shaderControls%22%3A%20%7B%22red_min%22%3A%200.0%2C%20%22red_max%22%3A%201356.0%2C%20%22green_min%22%3A%200.0%2C%20%22green_max%22%3A%203013.0%2C%20%22blue_min%22%3A%200.0%2C%20%22blue_max%22%3A%204095.0%7D%2C%20%22source%22%3A%20%7B%22url%22%3A%20%22zarr%3A//s3%3A//tissuecyte-ome-zarr-poc/40_128_128/1240649363%22%2C%20%22transform%22%3A%20%7B%22outputDimensions%22%3A%20%7B%22c%5E%22%3A%20%5B1%2C%20%22%22%5D%2C%20%22z%22%3A%20%5B0.0001%2C%20%22m%22%5D%2C%20%22y%22%3A%20%5B3.5e-07%2C%20%22m%22%5D%2C%20%22x%22%3A%20%5B3.5e-07%2C%20%22m%22%5D%7D%7D%7D%2C%20%22channelDimensions%22%3A%20%7B%22c%5E%22%3A%20%5B1%2C%20%22%22%5D%7D%2C%20%22name%22%3A%20%221240649363%20%2840_128_128%29%22%2C%20%22opacity%22%3A%201%7D%5D%7D"
+ function: 'get_neuroglancer_url',
+ params: {
+ blue_max: 4095.0,
+ blue_min: 0.0,
+ cross_section_scale: 57.142857142857146,
+ green_max: 3013.0,
+ green_min: 0.0,
+ img_name: '1240649363 (40_128_128)',
+ layout: '4panel',
+ red_max: 1356.0,
+ red_min: 0.0,
+ src_url: 'zarr://s3://tissuecyte-ome-zarr-poc/40_128_128/1240649363',
+ x_mm: 0.00035,
+ y_mm: 0.00035,
+ z_mm: 0.1,
+ },
+ type: 'Single image series; all three planes',
+ url: 'https://neuroglancer-demo.appspot.com/#!%7B%22dimensions%22%3A%20%7B%22x%22%3A%20%5B3.5e-07%2C%20%22m%22%5D%2C%20%22y%22%3A%20%5B3.5e-07%2C%20%22m%22%5D%2C%20%22z%22%3A%20%5B0.0001%2C%20%22m%22%5D%7D%2C%20%22crossSectionScale%22%3A%2057.142857142857146%2C%20%22projectionScale%22%3A%2040000%2C%20%22selectedLayer%22%3A%20%7B%22visible%22%3A%20true%2C%20%22layer%22%3A%20%221240649363%20%2840_128_128%29%22%7D%2C%20%22layout%22%3A%20%224panel%22%2C%20%22layers%22%3A%20%5B%7B%22type%22%3A%20%22image%22%2C%20%22tab%22%3A%20%22rendering%22%2C%20%22shader%22%3A%20%22%5Cn%20%20%20%20%23uicontrol%20float%20red_min%20slider%28min%3D0.0%2C%20max%3D2712.0%29%5Cn%20%20%20%20%23uicontrol%20float%20red_max%20slider%28min%3D0.0%2C%20max%3D2712.0%29%5Cn%20%20%20%20%23uicontrol%20float%20green_min%20slider%28min%3D0.0%2C%20max%3D6026.0%29%5Cn%20%20%20%20%23uicontrol%20float%20green_max%20slider%28min%3D0.0%2C%20max%3D6026.0%29%5Cn%20%20%20%20%23uicontrol%20float%20blue_min%20slider%28min%3D0.0%2C%20max%3D8190.0%29%5Cn%20%20%20%20%23uicontrol%20float%20blue_max%20slider%28min%3D0.0%2C%20max%3D8190.0%29%5Cn%20%20%20%20%23uicontrol%20bool%20red_visible%20checkbox%28default%3Dtrue%29%3B%5Cn%20%20%20%20%23uicontrol%20bool%20green_visible%20checkbox%28default%3Dtrue%29%3B%5Cn%20%20%20%20%23uicontrol%20bool%20blue_visible%20checkbox%28default%3Dtrue%29%3B%5Cn%20%20%20%20%5Cn%20%20%20%20void%20main%28%29%20%7B%5Cn%20%20%20%20%20%20%20%20float%20r%3B%5Cn%20%20%20%20%20%20%20%20float%20r_scale%3Dred_max-red_min%3B%5Cn%20%20%20%20%20%20%20%20if%28%21red_visible%20%7C%7C%20%28r_scale%3C%3D0.0%29%20%29%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20r%3D0.0%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20else%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20r%3D%28float%28getDataValue%280%29.value%29-red_min%29/r_scale%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20if%28r%3E1.0%29r%3D1.0%3B%5Cn%5Cn%20%20%20%20%20%20%20%20%20float%20g%3B%5Cn%20%20%20%20%20%20%20%20%20float%20g_scale%3Dgreen_max-green_min%3B%5Cn%20%20%20%20%20%20%20%20%20if%28%21green_visible%20%7C%7C%20%28g_scale%3C%3D0.0%29%29%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20g%3D0.0%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20else%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20g%3D%28float%28getDataValue%281%29.value%29-green_min%29/g_scale%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20if%28g%3E1.0%29g%3D1.0%3B%5Cn%5Cn%20%20%20%20%20%20%20%20%20float%20b%3B%5Cn%20%20%20%20%20%20%20%20%20float%20b_scale%3Dblue_max-blue_min%3B%5Cn%20%20%20%20%20%20%20%20%20if%28%21blue_visible%20%7C%7C%20%28b_scale%3C%3D0.0%29%29%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20b%3D0.0%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20else%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20b%3D%28float%28getDataValue%282%29.value%29-blue_min%29/b_scale%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20if%28b%3E1.0%29b%3D1.0%3B%5Cn%5Cn%20%20%20%20%20%20%20%20%20emitRGB%28vec3%28r%2Cg%2Cb%29%29%3B%5Cn%20%20%20%20%20%7D%5Cn%20%20%20%20%20%22%2C%20%22shaderControls%22%3A%20%7B%22red_min%22%3A%200.0%2C%20%22red_max%22%3A%201356.0%2C%20%22green_min%22%3A%200.0%2C%20%22green_max%22%3A%203013.0%2C%20%22blue_min%22%3A%200.0%2C%20%22blue_max%22%3A%204095.0%7D%2C%20%22source%22%3A%20%7B%22url%22%3A%20%22zarr%3A//s3%3A//tissuecyte-ome-zarr-poc/40_128_128/1240649363%22%2C%20%22transform%22%3A%20%7B%22outputDimensions%22%3A%20%7B%22c%5E%22%3A%20%5B1%2C%20%22%22%5D%2C%20%22z%22%3A%20%5B0.0001%2C%20%22m%22%5D%2C%20%22y%22%3A%20%5B3.5e-07%2C%20%22m%22%5D%2C%20%22x%22%3A%20%5B3.5e-07%2C%20%22m%22%5D%7D%7D%7D%2C%20%22channelDimensions%22%3A%20%7B%22c%5E%22%3A%20%5B1%2C%20%22%22%5D%7D%2C%20%22name%22%3A%20%221240649363%20%2840_128_128%29%22%2C%20%22opacity%22%3A%201%7D%5D%7D',
},
{
- "function": "get_neuroglancer_url",
- "params": {
- "blue_max": 4095.0,
- "blue_min": 0.0,
- "cross_section_scale": 37.714285714285715,
- "green_max": 3013.0,
- "green_min": 0.0,
- "img_name": "1240649363 (40_128_128)",
- "layout": "xy",
- "red_max": 1356.0,
- "red_min": 0.0,
- "src_url": "zarr://s3://tissuecyte-ome-zarr-poc/40_128_128/1240649363",
- "x_mm": 0.00035,
- "y_mm": 0.00035,
- "z_mm": 0.1
- },
- "type": "Single image series; coronal projection",
- "url": "https://neuroglancer-demo.appspot.com/#!%7B%22dimensions%22%3A%20%7B%22x%22%3A%20%5B3.5e-07%2C%20%22m%22%5D%2C%20%22y%22%3A%20%5B3.5e-07%2C%20%22m%22%5D%2C%20%22z%22%3A%20%5B0.0001%2C%20%22m%22%5D%7D%2C%20%22crossSectionScale%22%3A%2037.714285714285715%2C%20%22projectionScale%22%3A%2040000%2C%20%22selectedLayer%22%3A%20%7B%22visible%22%3A%20true%2C%20%22layer%22%3A%20%221240649363%20%2840_128_128%29%22%7D%2C%20%22layout%22%3A%20%22xy%22%2C%20%22layers%22%3A%20%5B%7B%22type%22%3A%20%22image%22%2C%20%22tab%22%3A%20%22rendering%22%2C%20%22shader%22%3A%20%22%5Cn%20%20%20%20%23uicontrol%20float%20red_min%20slider%28min%3D0.0%2C%20max%3D2712.0%29%5Cn%20%20%20%20%23uicontrol%20float%20red_max%20slider%28min%3D0.0%2C%20max%3D2712.0%29%5Cn%20%20%20%20%23uicontrol%20float%20green_min%20slider%28min%3D0.0%2C%20max%3D6026.0%29%5Cn%20%20%20%20%23uicontrol%20float%20green_max%20slider%28min%3D0.0%2C%20max%3D6026.0%29%5Cn%20%20%20%20%23uicontrol%20float%20blue_min%20slider%28min%3D0.0%2C%20max%3D8190.0%29%5Cn%20%20%20%20%23uicontrol%20float%20blue_max%20slider%28min%3D0.0%2C%20max%3D8190.0%29%5Cn%20%20%20%20%23uicontrol%20bool%20red_visible%20checkbox%28default%3Dtrue%29%3B%5Cn%20%20%20%20%23uicontrol%20bool%20green_visible%20checkbox%28default%3Dtrue%29%3B%5Cn%20%20%20%20%23uicontrol%20bool%20blue_visible%20checkbox%28default%3Dtrue%29%3B%5Cn%20%20%20%20%5Cn%20%20%20%20void%20main%28%29%20%7B%5Cn%20%20%20%20%20%20%20%20float%20r%3B%5Cn%20%20%20%20%20%20%20%20float%20r_scale%3Dred_max-red_min%3B%5Cn%20%20%20%20%20%20%20%20if%28%21red_visible%20%7C%7C%20%28r_scale%3C%3D0.0%29%20%29%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20r%3D0.0%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20else%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20r%3D%28float%28getDataValue%280%29.value%29-red_min%29/r_scale%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20if%28r%3E1.0%29r%3D1.0%3B%5Cn%5Cn%20%20%20%20%20%20%20%20%20float%20g%3B%5Cn%20%20%20%20%20%20%20%20%20float%20g_scale%3Dgreen_max-green_min%3B%5Cn%20%20%20%20%20%20%20%20%20if%28%21green_visible%20%7C%7C%20%28g_scale%3C%3D0.0%29%29%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20g%3D0.0%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20else%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20g%3D%28float%28getDataValue%281%29.value%29-green_min%29/g_scale%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20if%28g%3E1.0%29g%3D1.0%3B%5Cn%5Cn%20%20%20%20%20%20%20%20%20float%20b%3B%5Cn%20%20%20%20%20%20%20%20%20float%20b_scale%3Dblue_max-blue_min%3B%5Cn%20%20%20%20%20%20%20%20%20if%28%21blue_visible%20%7C%7C%20%28b_scale%3C%3D0.0%29%29%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20b%3D0.0%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20else%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20b%3D%28float%28getDataValue%282%29.value%29-blue_min%29/b_scale%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20if%28b%3E1.0%29b%3D1.0%3B%5Cn%5Cn%20%20%20%20%20%20%20%20%20emitRGB%28vec3%28r%2Cg%2Cb%29%29%3B%5Cn%20%20%20%20%20%7D%5Cn%20%20%20%20%20%22%2C%20%22shaderControls%22%3A%20%7B%22red_min%22%3A%200.0%2C%20%22red_max%22%3A%201356.0%2C%20%22green_min%22%3A%200.0%2C%20%22green_max%22%3A%203013.0%2C%20%22blue_min%22%3A%200.0%2C%20%22blue_max%22%3A%204095.0%7D%2C%20%22source%22%3A%20%7B%22url%22%3A%20%22zarr%3A//s3%3A//tissuecyte-ome-zarr-poc/40_128_128/1240649363%22%2C%20%22transform%22%3A%20%7B%22outputDimensions%22%3A%20%7B%22c%5E%22%3A%20%5B1%2C%20%22%22%5D%2C%20%22z%22%3A%20%5B0.0001%2C%20%22m%22%5D%2C%20%22y%22%3A%20%5B3.5e-07%2C%20%22m%22%5D%2C%20%22x%22%3A%20%5B3.5e-07%2C%20%22m%22%5D%7D%7D%7D%2C%20%22channelDimensions%22%3A%20%7B%22c%5E%22%3A%20%5B1%2C%20%22%22%5D%7D%2C%20%22name%22%3A%20%221240649363%20%2840_128_128%29%22%2C%20%22opacity%22%3A%201%7D%5D%7D"
+ function: 'get_neuroglancer_url',
+ params: {
+ blue_max: 4095.0,
+ blue_min: 0.0,
+ cross_section_scale: 37.714285714285715,
+ green_max: 3013.0,
+ green_min: 0.0,
+ img_name: '1240649363 (40_128_128)',
+ layout: 'xy',
+ red_max: 1356.0,
+ red_min: 0.0,
+ src_url: 'zarr://s3://tissuecyte-ome-zarr-poc/40_128_128/1240649363',
+ x_mm: 0.00035,
+ y_mm: 0.00035,
+ z_mm: 0.1,
+ },
+ type: 'Single image series; coronal projection',
+ url: 'https://neuroglancer-demo.appspot.com/#!%7B%22dimensions%22%3A%20%7B%22x%22%3A%20%5B3.5e-07%2C%20%22m%22%5D%2C%20%22y%22%3A%20%5B3.5e-07%2C%20%22m%22%5D%2C%20%22z%22%3A%20%5B0.0001%2C%20%22m%22%5D%7D%2C%20%22crossSectionScale%22%3A%2037.714285714285715%2C%20%22projectionScale%22%3A%2040000%2C%20%22selectedLayer%22%3A%20%7B%22visible%22%3A%20true%2C%20%22layer%22%3A%20%221240649363%20%2840_128_128%29%22%7D%2C%20%22layout%22%3A%20%22xy%22%2C%20%22layers%22%3A%20%5B%7B%22type%22%3A%20%22image%22%2C%20%22tab%22%3A%20%22rendering%22%2C%20%22shader%22%3A%20%22%5Cn%20%20%20%20%23uicontrol%20float%20red_min%20slider%28min%3D0.0%2C%20max%3D2712.0%29%5Cn%20%20%20%20%23uicontrol%20float%20red_max%20slider%28min%3D0.0%2C%20max%3D2712.0%29%5Cn%20%20%20%20%23uicontrol%20float%20green_min%20slider%28min%3D0.0%2C%20max%3D6026.0%29%5Cn%20%20%20%20%23uicontrol%20float%20green_max%20slider%28min%3D0.0%2C%20max%3D6026.0%29%5Cn%20%20%20%20%23uicontrol%20float%20blue_min%20slider%28min%3D0.0%2C%20max%3D8190.0%29%5Cn%20%20%20%20%23uicontrol%20float%20blue_max%20slider%28min%3D0.0%2C%20max%3D8190.0%29%5Cn%20%20%20%20%23uicontrol%20bool%20red_visible%20checkbox%28default%3Dtrue%29%3B%5Cn%20%20%20%20%23uicontrol%20bool%20green_visible%20checkbox%28default%3Dtrue%29%3B%5Cn%20%20%20%20%23uicontrol%20bool%20blue_visible%20checkbox%28default%3Dtrue%29%3B%5Cn%20%20%20%20%5Cn%20%20%20%20void%20main%28%29%20%7B%5Cn%20%20%20%20%20%20%20%20float%20r%3B%5Cn%20%20%20%20%20%20%20%20float%20r_scale%3Dred_max-red_min%3B%5Cn%20%20%20%20%20%20%20%20if%28%21red_visible%20%7C%7C%20%28r_scale%3C%3D0.0%29%20%29%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20r%3D0.0%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20else%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20r%3D%28float%28getDataValue%280%29.value%29-red_min%29/r_scale%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20if%28r%3E1.0%29r%3D1.0%3B%5Cn%5Cn%20%20%20%20%20%20%20%20%20float%20g%3B%5Cn%20%20%20%20%20%20%20%20%20float%20g_scale%3Dgreen_max-green_min%3B%5Cn%20%20%20%20%20%20%20%20%20if%28%21green_visible%20%7C%7C%20%28g_scale%3C%3D0.0%29%29%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20g%3D0.0%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20else%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20g%3D%28float%28getDataValue%281%29.value%29-green_min%29/g_scale%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20if%28g%3E1.0%29g%3D1.0%3B%5Cn%5Cn%20%20%20%20%20%20%20%20%20float%20b%3B%5Cn%20%20%20%20%20%20%20%20%20float%20b_scale%3Dblue_max-blue_min%3B%5Cn%20%20%20%20%20%20%20%20%20if%28%21blue_visible%20%7C%7C%20%28b_scale%3C%3D0.0%29%29%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20b%3D0.0%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20else%7B%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20b%3D%28float%28getDataValue%282%29.value%29-blue_min%29/b_scale%3B%5Cn%20%20%20%20%20%20%20%20%20%7D%5Cn%20%20%20%20%20%20%20%20%20if%28b%3E1.0%29b%3D1.0%3B%5Cn%5Cn%20%20%20%20%20%20%20%20%20emitRGB%28vec3%28r%2Cg%2Cb%29%29%3B%5Cn%20%20%20%20%20%7D%5Cn%20%20%20%20%20%22%2C%20%22shaderControls%22%3A%20%7B%22red_min%22%3A%200.0%2C%20%22red_max%22%3A%201356.0%2C%20%22green_min%22%3A%200.0%2C%20%22green_max%22%3A%203013.0%2C%20%22blue_min%22%3A%200.0%2C%20%22blue_max%22%3A%204095.0%7D%2C%20%22source%22%3A%20%7B%22url%22%3A%20%22zarr%3A//s3%3A//tissuecyte-ome-zarr-poc/40_128_128/1240649363%22%2C%20%22transform%22%3A%20%7B%22outputDimensions%22%3A%20%7B%22c%5E%22%3A%20%5B1%2C%20%22%22%5D%2C%20%22z%22%3A%20%5B0.0001%2C%20%22m%22%5D%2C%20%22y%22%3A%20%5B3.5e-07%2C%20%22m%22%5D%2C%20%22x%22%3A%20%5B3.5e-07%2C%20%22m%22%5D%7D%7D%7D%2C%20%22channelDimensions%22%3A%20%7B%22c%5E%22%3A%20%5B1%2C%20%22%22%5D%7D%2C%20%22name%22%3A%20%221240649363%20%2840_128_128%29%22%2C%20%22opacity%22%3A%201%7D%5D%7D',
},
{
- "function": "get_contact_sheet_url",
- "params": {
- "blue_max": 4095.0,
- "blue_min": 0.0,
- "cross_section_scale": 576.0,
- "green_max": 3013.0,
- "green_min": 0.0,
- "img_name": "1240649363 (40_128_128)",
- "ome_zarr_shape": [
- 3,
- 142,
- 29998,
- 39998
- ],
- "red_max": 1356.0,
- "red_min": 0.0,
- "src_url": "zarr://s3://tissuecyte-ome-zarr-poc/40_128_128/1240649363",
- "x_mm": 0.00035,
- "y_mm": 0.00035,
- "z_mm": 0.1
- },
- "type": "Single image series; contact sheet",
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- }
- ]
\ No newline at end of file
+ function: 'get_contact_sheet_url',
+ params: {
+ blue_max: 4095.0,
+ blue_min: 0.0,
+ cross_section_scale: 576.0,
+ green_max: 3013.0,
+ green_min: 0.0,
+ img_name: '1240649363 (40_128_128)',
+ ome_zarr_shape: [3, 142, 29998, 39998],
+ red_max: 1356.0,
+ red_min: 0.0,
+ src_url: 'zarr://s3://tissuecyte-ome-zarr-poc/40_128_128/1240649363',
+ x_mm: 0.00035,
+ y_mm: 0.00035,
+ z_mm: 0.1,
+ },
+ type: 'Single image series; contact sheet',
+ url: 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ltSubsources%22%3A%20false%7D%2C%20%7B%22url%22%3A%20%22zarr%3A//s3%3A//tissuecyte-ome-zarr-poc/40_128_128/1240649363%22%2C%20%22transform%22%3A%20%7B%22outputDimensions%22%3A%20%7B%22c%5E%22%3A%20%5B1%2C%20%22%22%5D%2C%20%22z%22%3A%20%5B0.0001%2C%20%22m%22%5D%2C%20%22y%22%3A%20%5B3.5e-07%2C%20%22m%22%5D%2C%20%22x%22%3A%20%5B3.5e-07%2C%20%22m%22%5D%7D%2C%20%22matrix%22%3A%20%5B%5B1%2C%200%2C%200%2C%200%2C%200%5D%2C%20%5B0%2C%20-1%2C%200%2C%200%2C%20-137%5D%2C%20%5B0%2C%200%2C%201%2C%200%2C%20329978%5D%2C%20%5B0%2C%200%2C%200%2C%201%2C%20199990%5D%5D%7D%2C%20%22subsources%22%3A%20%7B%22default%22%3A%20true%7D%2C%20%22enableDefaultSubsources%22%3A%20false%7D%2C%20%7B%22url%22%3A%20%22zarr%3A//s3%3A//tissuecyte-ome-zarr-poc/40_128_128/1240649363%22%2C%20%22transform%22%3A%20%7B%22outputDimensions%22%3A%20%7B%22c%5E%22%3A%20%5B1%2C%20%22%22%5D%2C%20%22z%22%3A%20%5B0.0001%2C%20%22m%22%5D%2C%20%22y%22%3A%20%5B3.5e-07%2C%20%22m%22%5D%2C%20%22x%22%3A%20%5B3.5e-07%2C%20%22m%22%5D%7D%2C%20%22matrix%22%3A%20%5B%5B1%2C%200%2C%200%2C%200%2C%200%5D%2C%20%5B0%2C%20-1%2C%200%2C%200%2C%20-138%5D%2C%20%5B0%2C%200%2C%201%2C%200%2C%20329978%5D%2C%20%5B0%2C%200%2C%200%2C%201%2C%20239988%5D%5D%7D%2C%20%22subsources%22%3A%20%7B%22default%22%3A%20true%7D%2C%20%22enableDefaultSubsources%22%3A%20false%7D%2C%20%7B%22url%22%3A%20%22zarr%3A//s3%3A//tissuecyte-ome-zarr-poc/40_128_128/1240649363%22%2C%20%22transform%22%3A%20%7B%22outputDimensions%22%3A%20%7B%22c%5E%22%3A%20%5B1%2C%20%22%22%5D%2C%20%22z%22%3A%20%5B0.0001%2C%20%22m%22%5D%2C%20%22y%22%3A%20%5B3.5e-07%2C%20%22m%22%5D%2C%20%22x%22%3A%20%5B3.5e-07%2C%20%22m%22%5D%7D%2C%20%22matrix%22%3A%20%5B%5B1%2C%200%2C%200%2C%200%2C%200%5D%2C%20%5B0%2C%20-1%2C%200%2C%200%2C%20-139%5D%2C%20%5B0%2C%200%2C%201%2C%200%2C%20329978%5D%2C%20%5B0%2C%200%2C%200%2C%201%2C%20279986%5D%5D%7D%2C%20%22subsources%22%3A%20%7B%22default%22%3A%20true%7D%2C%20%22enableDefaultSubsources%22%3A%20false%7D%2C%20%7B%22url%22%3A%20%22zarr%3A//s3%3A//tissuecyte-ome-zarr-poc/40_128_128/1240649363%22%2C%20%22transform%22%3A%20%7B%22outputDimensions%22%3A%20%7B%22c%5E%22%3A%20%5B1%2C%20%22%22%5D%2C%20%22z%22%3A%20%5B0.0001%2C%20%22m%22%5D%2C%20%22y%22%3A%20%5B3.5e-07%2C%20%22m%22%5D%2C%20%22x%22%3A%20%5B3.5e-07%2C%20%22m%22%5D%7D%2C%20%22matrix%22%3A%20%5B%5B1%2C%200%2C%200%2C%200%2C%200%5D%2C%20%5B0%2C%20-1%2C%200%2C%200%2C%20-140%5D%2C%20%5B0%2C%200%2C%201%2C%200%2C%20329978%5D%2C%20%5B0%2C%200%2C%200%2C%201%2C%20319984%5D%5D%7D%2C%20%22subsources%22%3A%20%7B%22default%22%3A%20true%7D%2C%20%22enableDefaultSubsources%22%3A%20false%7D%2C%20%7B%22url%22%3A%20%22zarr%3A//s3%3A//tissuecyte-ome-zarr-poc/40_128_128/1240649363%22%2C%20%22transform%22%3A%20%7B%22outputDimensions%22%3A%20%7B%22c%5E%22%3A%20%5B1%2C%20%22%22%5D%2C%20%22z%22%3A%20%5B0.0001%2C%20%22m%22%5D%2C%20%22y%22%3A%20%5B3.5e-07%2C%20%22m%22%5D%2C%20%22x%22%3A%20%5B3.5e-07%2C%20%22m%22%5D%7D%2C%20%22matrix%22%3A%20%5B%5B1%2C%200%2C%200%2C%200%2C%200%5D%2C%20%5B0%2C%20-1%2C%200%2C%200%2C%20-141%5D%2C%20%5B0%2C%200%2C%201%2C%200%2C%20329978%5D%2C%20%5B0%2C%200%2C%200%2C%201%2C%20359982%5D%5D%7D%2C%20%22subsources%22%3A%20%7B%22default%22%3A%20true%7D%2C%20%22enableDefaultSubsources%22%3A%20false%7D%5D%2C%20%22channelDimensions%22%3A%20%7B%22c%5E%22%3A%20%5B1%2C%20%22%22%5D%7D%2C%20%22name%22%3A%20%221240649363%20%2840_128_128%29%22%2C%20%22opacity%22%3A%201%7D%5D%2C%20%22velocity%22%3A%20%7B%22z%22%3A%20%7B%22velocity%22%3A%20-10%2C%20%22atBoundary%22%3A%20%22reverse%22%7D%7D%2C%20%22position%22%3A%20%5B239988%2C%20179988%2C%20-141%5D%7D',
+ },
+];
diff --git a/apps/neuroglancer-url/tsconfig.json b/apps/neuroglancer-url/tsconfig.json
index e5bee2e..0f20604 100644
--- a/apps/neuroglancer-url/tsconfig.json
+++ b/apps/neuroglancer-url/tsconfig.json
@@ -1,5 +1,4 @@
{
"extends": "../tsconfig.json",
"include": ["./src/**/*", "../common/src/**/*"]
-
-}
\ No newline at end of file
+}
diff --git a/apps/omezarr-viewer/README.md b/apps/omezarr-viewer/README.md
index 1a525dd..a7e14d8 100644
--- a/apps/omezarr-viewer/README.md
+++ b/apps/omezarr-viewer/README.md
@@ -1,8 +1,11 @@
## Ome-Zarr Viewer Demo
a very minimal demo to show how one might use the scatterbrain package to render volumetric images contained in an OME-zarr "File". Note that the datasets in the demos (there are 2) are hard-coded to some data in public S3 buckets.
+
### Versa
+
to run the versa demo, assuming you've just cloned this repository:
+
1. run `pnpm build` from the root directory
2. run `pnpm install` in this (apps/omezarr-viewer/) directory
3. run `pnpm run versa` in this directory
@@ -12,21 +15,25 @@ to run the versa demo, assuming you've just cloned this repository:
The app will load, and immediately begin requesting chunks from the versa dataset - you should be able to pan and zoom with the scroll-Wheel / mouse, and you should see a very basic set of UI controls. The versa dataset is a multi-channel "sequence of images" modality - so a list of available slices will be displayed, allowing the user to click on one to view it. RGB channels can be manipulated individually.
#### For developers
+
if you are interested in the code - you can start at the top: versa.ts contains the top-level glue code (its rather... demo-y! apologies for that - you should understand that this area of code is not "the point" - its just a short, easy-to-write harness for the good stuff) that makes the whole thing run. The interesting parts are probably in the neighborhood of `renderFrameHelper(...)`. The pattern we're looking for is:
+
1. get the chunks of data (or rather, handles to that data) which are in view with `getVisibleTiles`
2. create a frame to render those tiles, using the current view & other settings, using `beginLongRunningFrame`
3. now you have an object (we call it a frame) that represents rendering progress - you can cancel the frame, put it in a list, create a promise to do something when its over, whatever you like! the point is that it is a first class entity which lets you abstract away a great deal of uncertainty and complexity. As long as you targeted a private render target, nothing else that happens in the app can have any impact on the image being rendered by this frame.
4. Still reading? you might be interested in the "plugin-style" renderer which actually renders chunks of ome-zarr data - take a look at `versa-renderer.ts` which contain the "strategy" components of rendering:
-
- a. given a "camera" and a dataset, get me all the tasks (in our case, chunks of images) for what is in view: `getVisibleTiles`
- b. given a handle to a "chunk" fetch the chunk and associate it with how it will be used during rendering: `requestsForTile()`
- c. given fully-fetched data for a tile, render it! `buildVersaRenderer` - in this case we use [REgl](https://github.com/regl-project/regl/blob/master/API.md), an excellent WebGL abstraction layer, but the point of this plug-ability is that any user of the scatterbrain components may use whatever low-level rendering system (or data format) they prefer!
+
+ a. given a "camera" and a dataset, get me all the tasks (in our case, chunks of images) for what is in view: `getVisibleTiles`
+ b. given a handle to a "chunk" fetch the chunk and associate it with how it will be used during rendering: `requestsForTile()`
+ c. given fully-fetched data for a tile, render it! `buildVersaRenderer` - in this case we use [REgl](https://github.com/regl-project/regl/blob/master/API.md), an excellent WebGL abstraction layer, but the point of this plug-ability is that any user of the scatterbrain components may use whatever low-level rendering system (or data format) they prefer!
+
### Tissuecyte
+
to run the Tissuecyte demo, assuming you've just cloned this repository:
+
1. run `pnpm build` from the root directory
2. run `pnpm install` in this (apps/omezarr-viewer/) directory
3. run `pnpm run tissuecyte` in this directory
4. navigate to apps/omezarr-viewer/dst/ using your File browser / finder, and open `tissuecyte.html` in your browser.
-
-The app will load, and immediately begin requesting chunks from the tissuecyte dataset - you should be able to pan and zoom with the scrollwheel / mouse, and you should see a very basic set of UI controls. The tissuecyte dataset is a "Volume" mode dataset - you get a single channel (gray-scale), and you can scroll through slices of the volume with Alt+Scroll, or use the slider in the UI. Note that in both demos, very little work was done to provide a "production ready" experience - the screen will go black in places where data it needs to render is not yet available, it may be flickery. In particular, the limit on cache memory is quite low, so delays while waiting for data to be (re) downloaded are to be expected.
\ No newline at end of file
+The app will load, and immediately begin requesting chunks from the tissuecyte dataset - you should be able to pan and zoom with the scrollwheel / mouse, and you should see a very basic set of UI controls. The tissuecyte dataset is a "Volume" mode dataset - you get a single channel (gray-scale), and you can scroll through slices of the volume with Alt+Scroll, or use the slider in the UI. Note that in both demos, very little work was done to provide a "production ready" experience - the screen will go black in places where data it needs to render is not yet available, it may be flickery. In particular, the limit on cache memory is quite low, so delays while waiting for data to be (re) downloaded are to be expected.
diff --git a/apps/omezarr-viewer/package.json b/apps/omezarr-viewer/package.json
index 4abed12..9eed628 100644
--- a/apps/omezarr-viewer/package.json
+++ b/apps/omezarr-viewer/package.json
@@ -1,52 +1,52 @@
{
- "name": "@alleninstitute/vis-omezarr-demo",
- "version": "0.0.1",
- "contributors": [
- {
- "name": "Lane Sawyer",
- "email": "lane.sawyer@alleninstitute.org"
+ "name": "@alleninstitute/vis-omezarr-demo",
+ "version": "0.0.1",
+ "contributors": [
+ {
+ "name": "Lane Sawyer",
+ "email": "lane.sawyer@alleninstitute.org"
+ },
+ {
+ "name": "James Gerstenberger",
+ "email": "james.gerstenberger@alleninstitute.org"
+ },
+ {
+ "name": "Noah Shepard",
+ "email": "noah.shepard@alleninstitute.org"
+ },
+ {
+ "name": "Skyler Moosman",
+ "email": "skyler.moosman@alleninstitute.org"
+ },
+ {
+ "name": "Su Li",
+ "email": "su.li@alleninstitute.org"
+ }
+ ],
+ "license": "TBD",
+ "type": "module",
+ "main": "lib/index.js",
+ "types": "lib/index.d.ts",
+ "private": true,
+ "scripts": {
+ "preinstall": "npx only-allow pnpm",
+ "typecheck": "tsc --noEmit",
+ "demo": "esbuild src/demo.ts --bundle --outfile=dst/demo.js && cp public/* dst/",
+ "versa": "esbuild src/versa.ts --bundle --outfile=dst/versa.js && cp public/* dst/",
+ "tissuecyte": "esbuild src/tissuecyte.ts --bundle --outfile=dst/tissuecyte.js && cp public/* dst/",
+ "test": "jest --config=jest.config.cjs --watch"
},
- {
- "name": "James Gerstenberger",
- "email": "james.gerstenberger@alleninstitute.org"
+ "devDependencies": {
+ "esbuild": "^0.19.12",
+ "typescript": "^5.3.3"
},
- {
- "name": "Noah Shepard",
- "email": "noah.shepard@alleninstitute.org"
- },
- {
- "name": "Skyler Moosman",
- "email": "skyler.moosman@alleninstitute.org"
- },
- {
- "name": "Su Li",
- "email": "su.li@alleninstitute.org"
+ "dependencies": {
+ "@alleninstitute/vis-geometry": "workspace:*",
+ "@alleninstitute/vis-scatterbrain": "workspace:*",
+ "@types/lodash": "^4.14.202",
+ "@zhobo63/imgui-ts": "^0.1.43",
+ "lodash": "^4.17.21",
+ "regl": "^2.1.0",
+ "zarr": "^0.6.2"
}
- ],
- "license": "TBD",
- "type": "module",
- "main": "lib/index.js",
- "types": "lib/index.d.ts",
- "private": true,
- "scripts": {
- "preinstall": "npx only-allow pnpm",
- "typecheck": "tsc --noEmit",
- "demo": "esbuild src/demo.ts --bundle --outfile=dst/demo.js && cp public/* dst/",
- "versa": "esbuild src/versa.ts --bundle --outfile=dst/versa.js && cp public/* dst/",
- "tissuecyte": "esbuild src/tissuecyte.ts --bundle --outfile=dst/tissuecyte.js && cp public/* dst/",
- "test": "jest --config=jest.config.cjs --watch"
- },
- "devDependencies": {
- "esbuild": "^0.19.12",
- "typescript": "^5.3.3"
- },
- "dependencies": {
- "@alleninstitute/vis-geometry": "workspace:*",
- "@alleninstitute/vis-scatterbrain": "workspace:*",
- "@types/lodash": "^4.14.202",
- "@zhobo63/imgui-ts": "^0.1.43",
- "lodash": "^4.17.21",
- "regl": "^2.1.0",
- "zarr": "^0.6.2"
- }
-}
\ No newline at end of file
+}
diff --git a/apps/omezarr-viewer/public/tissuecyte.html b/apps/omezarr-viewer/public/tissuecyte.html
index 5cd56e5..1f15c28 100644
--- a/apps/omezarr-viewer/public/tissuecyte.html
+++ b/apps/omezarr-viewer/public/tissuecyte.html
@@ -1,8 +1,14 @@
-
+
-
-
-
-
+
+
+
+
diff --git a/apps/omezarr-viewer/public/versa.html b/apps/omezarr-viewer/public/versa.html
index 9821564..8c25eb8 100644
--- a/apps/omezarr-viewer/public/versa.html
+++ b/apps/omezarr-viewer/public/versa.html
@@ -1,7 +1,10 @@
-
-
-
-
-
-
-
+
+
+
+
+
+
+
diff --git a/apps/omezarr-viewer/src/annotation/path.ts b/apps/omezarr-viewer/src/annotation/path.ts
index f0ff00e..1bb5aa2 100644
--- a/apps/omezarr-viewer/src/annotation/path.ts
+++ b/apps/omezarr-viewer/src/annotation/path.ts
@@ -1,99 +1,97 @@
-import type { vec2, vec4 } from "@alleninstitute/vis-geometry"
-
-export type Point = {
- point: vec2;
- pressure?: number;
-}
-// type SLLNode
= {
-// item: T;
-// next: SLLNode | null;
-// }
-// type SLL = {
-// head: SLLNode|null;
-// tail: SLLNode|null;
-// length
-// }
-export type Pen = {
- color: vec4;
- strokeWidth: number;
-}
-export type PathAnnotation = {
- path: Point[];
- pen: Pen;
-}
-
-// make a set of handlers that make a thing drawable...
-
-
-// how would we generify drawing on top of something...
-export type DrawingHost = {
- updateCurrentStroke: (point: Point) => void;
- newStroke: (point: Point) => void;
- // endStroke?
- currentTool: () => Pen | 'camera';
- pan: (screenDelta: vec2) => void;
- screenToDataSpace: (screen: vec2) => vec2;
- screenWidthToDataWidth: (w: number) => number;
-}
-
-export function initDrawableInterface(surface: HTMLElement, host: DrawingHost) {
- let buttonDown: boolean = false;
- let curPointerId: number | null;
-
- surface.onpointermove = (ev: PointerEvent) => {
- if (buttonDown && ev.pointerId === curPointerId) {
- if (host.currentTool() == 'camera') {
- // pan that camera!
- host.pan([ev.movementX, ev.movementY])
- } else {
- // draw with our current pen... hmmmm
- host.updateCurrentStroke({
- point: host.screenToDataSpace([ev.x, ev.y]),
- pressure: ev.pressure
- })
- }
- }
- }
- surface.onpointerdown = (ev: PointerEvent) => {
- if (curPointerId === null) {
- curPointerId = ev.pointerId;
- buttonDown = true;
- if (host.currentTool() !== 'camera') {
- host.newStroke({
- point: host.screenToDataSpace([ev.x, ev.y]),
- pressure: ev.pressure
- })
- }
- }
- }
- surface.onpointerup = (ev: PointerEvent) => {
- if (curPointerId === ev.pointerId) {
- curPointerId = null;
- buttonDown = false;
- }
- }
-
-
- return () => {
- // cleanup!
- // todo!
- }
-}
-
-// export function beginDrawing(pen: Pen, p: vec2, pressure?: number): PathAnnotation {
-// return {
-// pen,
-// path: [{
-// point: p,
-// pressure: pressure ?? 1.0
-// }]
-// }
-// }
-// export function continueDrawing(annotation: PathAnnotation, p: vec2, pressure?: number): PathAnnotation {
-// return {
-// ...annotation, path: [...annotation.path, {
-// point: p,
-// pressure: pressure ?? 1.0
-// }]
-// }
-// }
+import type { vec2, vec4 } from '@alleninstitute/vis-geometry';
+
+export type Point = {
+ point: vec2;
+ pressure?: number;
+};
+// type SLLNode = {
+// item: T;
+// next: SLLNode | null;
+// }
+// type SLL = {
+// head: SLLNode|null;
+// tail: SLLNode|null;
+// length
+// }
+export type Pen = {
+ color: vec4;
+ strokeWidth: number;
+};
+export type PathAnnotation = {
+ path: Point[];
+ pen: Pen;
+};
+
+// make a set of handlers that make a thing drawable...
+
+// how would we generify drawing on top of something...
+export type DrawingHost = {
+ updateCurrentStroke: (point: Point) => void;
+ newStroke: (point: Point) => void;
+ // endStroke?
+ currentTool: () => Pen | 'camera';
+ pan: (screenDelta: vec2) => void;
+ screenToDataSpace: (screen: vec2) => vec2;
+ screenWidthToDataWidth: (w: number) => number;
+};
+
+export function initDrawableInterface(surface: HTMLElement, host: DrawingHost) {
+ let buttonDown: boolean = false;
+ let curPointerId: number | null;
+
+ surface.onpointermove = (ev: PointerEvent) => {
+ if (buttonDown && ev.pointerId === curPointerId) {
+ if (host.currentTool() == 'camera') {
+ // pan that camera!
+ host.pan([ev.movementX, ev.movementY]);
+ } else {
+ // draw with our current pen... hmmmm
+ host.updateCurrentStroke({
+ point: host.screenToDataSpace([ev.x, ev.y]),
+ pressure: ev.pressure,
+ });
+ }
+ }
+ };
+ surface.onpointerdown = (ev: PointerEvent) => {
+ if (curPointerId === null) {
+ curPointerId = ev.pointerId;
+ buttonDown = true;
+ if (host.currentTool() !== 'camera') {
+ host.newStroke({
+ point: host.screenToDataSpace([ev.x, ev.y]),
+ pressure: ev.pressure,
+ });
+ }
+ }
+ };
+ surface.onpointerup = (ev: PointerEvent) => {
+ if (curPointerId === ev.pointerId) {
+ curPointerId = null;
+ buttonDown = false;
+ }
+ };
+
+ return () => {
+ // cleanup!
+ // todo!
+ };
+}
+
+// export function beginDrawing(pen: Pen, p: vec2, pressure?: number): PathAnnotation {
+// return {
+// pen,
+// path: [{
+// point: p,
+// pressure: pressure ?? 1.0
+// }]
+// }
+// }
+// export function continueDrawing(annotation: PathAnnotation, p: vec2, pressure?: number): PathAnnotation {
+// return {
+// ...annotation, path: [...annotation.path, {
+// point: p,
+// pressure: pressure ?? 1.0
+// }]
+// }
+// }
diff --git a/apps/omezarr-viewer/src/camera.ts b/apps/omezarr-viewer/src/camera.ts
index 5cda0b2..a73dfb5 100644
--- a/apps/omezarr-viewer/src/camera.ts
+++ b/apps/omezarr-viewer/src/camera.ts
@@ -1,9 +1,8 @@
-import type { box2D, vec2 } from "@alleninstitute/vis-geometry"
-
-// a basic camera, for viewing slices
-export type Camera = {
- readonly view: box2D; // a view in 'data space'
- readonly screen: vec2; // what that view projects to in display space, aka pixels
- readonly projection: 'webImage' | 'cartesian'
-}
-
+import type { box2D, vec2 } from '@alleninstitute/vis-geometry';
+
+// a basic camera, for viewing slices
+export type Camera = {
+ readonly view: box2D; // a view in 'data space'
+ readonly screen: vec2; // what that view projects to in display space, aka pixels
+ readonly projection: 'webImage' | 'cartesian';
+};
diff --git a/apps/omezarr-viewer/src/components/color-map.ts b/apps/omezarr-viewer/src/components/color-map.ts
index 280f09c..41aa90b 100644
--- a/apps/omezarr-viewer/src/components/color-map.ts
+++ b/apps/omezarr-viewer/src/components/color-map.ts
@@ -1,66 +1,66 @@
-// an IM-gui widget for controlling the display of a single channel
-
-// an IM-gui widget for controlling the display of a single channel
-import type { Interval } from "@alleninstitute/vis-geometry";
-import { ImGui } from "@zhobo63/imgui-ts";
-import type { ImTuple2 } from "@zhobo63/imgui-ts/src/bind-imgui";
-import { ImGuiColorEditFlags, ImGuiSliderFlags, ImVec4 } from "@zhobo63/imgui-ts/src/imgui";
-
-// assumes its mid-frame of an IMGui.newFrame() when called!
-
-export function colorMapWidget(
- channel: string,
- mutable: {
- useMe: boolean;
- color: ImVec4;
- gamut: Interval;
- index: number;
- },
- numChannels: number
-) {
- const channelChoices = new Array(numChannels).map((n) => n.toFixed(0));
- const getter = (data: string[], index: number, out: [string]) => {
- out[0] = data[index];
- return false;
- };
- let changed = false;
- const { gamut, color } = mutable;
- let index = mutable.index;
- const range: ImTuple2 = [gamut.min, gamut.max];
- if (
- ImGui.Checkbox("", (b?: boolean) => {
- mutable.useMe = b ?? mutable.useMe;
- return mutable.useMe;
- })
- ) {
- changed = true;
- }
- ImGui.SameLine();
- ImGui.ColorButton(" ", color, ImGuiColorEditFlags.NoAlpha);
- ImGui.SameLine();
- ImGui.PushItemWidth(10);
- if (
- ImGui.DragInt(
- `${channel}_options`,
- (i?: number) => {
- index = i ?? index;
- return index;
- },
- 0.2,
- 0,
- numChannels - 1,
- "%i"
- )
- ) {
- changed = true;
- mutable.index = index;
- }
- ImGui.PopItemWidth();
-
- ImGui.SameLine();
- if (ImGui.SliderFloat2(channel, range, 0, 9999, "%3f", ImGuiSliderFlags.Logarithmic)) {
- mutable.gamut = { min: range[0], max: range[1] };
- changed = true;
- }
- return { changed, ...mutable };
-}
+// an IM-gui widget for controlling the display of a single channel
+
+// an IM-gui widget for controlling the display of a single channel
+import type { Interval } from '@alleninstitute/vis-geometry';
+import { ImGui } from '@zhobo63/imgui-ts';
+import type { ImTuple2 } from '@zhobo63/imgui-ts/src/bind-imgui';
+import { ImGuiColorEditFlags, ImGuiSliderFlags, ImVec4 } from '@zhobo63/imgui-ts/src/imgui';
+
+// assumes its mid-frame of an IMGui.newFrame() when called!
+
+export function colorMapWidget(
+ channel: string,
+ mutable: {
+ useMe: boolean;
+ color: ImVec4;
+ gamut: Interval;
+ index: number;
+ },
+ numChannels: number
+) {
+ const channelChoices = new Array(numChannels).map((n) => n.toFixed(0));
+ const getter = (data: string[], index: number, out: [string]) => {
+ out[0] = data[index];
+ return false;
+ };
+ let changed = false;
+ const { gamut, color } = mutable;
+ let index = mutable.index;
+ const range: ImTuple2 = [gamut.min, gamut.max];
+ if (
+ ImGui.Checkbox('', (b?: boolean) => {
+ mutable.useMe = b ?? mutable.useMe;
+ return mutable.useMe;
+ })
+ ) {
+ changed = true;
+ }
+ ImGui.SameLine();
+ ImGui.ColorButton(' ', color, ImGuiColorEditFlags.NoAlpha);
+ ImGui.SameLine();
+ ImGui.PushItemWidth(10);
+ if (
+ ImGui.DragInt(
+ `${channel}_options`,
+ (i?: number) => {
+ index = i ?? index;
+ return index;
+ },
+ 0.2,
+ 0,
+ numChannels - 1,
+ '%i'
+ )
+ ) {
+ changed = true;
+ mutable.index = index;
+ }
+ ImGui.PopItemWidth();
+
+ ImGui.SameLine();
+ if (ImGui.SliderFloat2(channel, range, 0, 9999, '%3f', ImGuiSliderFlags.Logarithmic)) {
+ mutable.gamut = { min: range[0], max: range[1] };
+ changed = true;
+ }
+ return { changed, ...mutable };
+}
diff --git a/apps/omezarr-viewer/src/image-renderer.ts b/apps/omezarr-viewer/src/image-renderer.ts
index 0984187..0133cb7 100644
--- a/apps/omezarr-viewer/src/image-renderer.ts
+++ b/apps/omezarr-viewer/src/image-renderer.ts
@@ -1,67 +1,67 @@
-import type { vec2, vec4 } from "@alleninstitute/vis-geometry";
-import REGL, { type Framebuffer2D } from "regl";
-
-type Props = {
- target: Framebuffer2D | null;
- box: vec4;
- view: vec4;
- // viewport: REGL.BoundingBox;
- img: REGL.Texture2D | REGL.Framebuffer2D;
-};
-export function buildImageRenderer(regl: REGL.Regl) {
- const cmd = regl<
- { view: vec4; box: vec4; img: REGL.Texture2D | REGL.Framebuffer2D },
- { pos: REGL.BufferData },
- Props
- >({
- vert: ` precision highp float;
- attribute vec2 pos;
-
- uniform vec4 view;
- uniform vec4 box;
- varying vec2 texCoord;
-
- void main(){
- vec2 tileSize = box.zw-box.xy;
- texCoord = pos;
- vec2 obj = (pos.xy*tileSize+box.xy);
- vec2 p = (obj-view.xy)/(view.zw-view.xy);
- // now, to clip space
- p = (p*2.0)-1.0;
- gl_Position = vec4(p.x,p.y,0.0,1.0);
- }`,
- frag: `
- precision highp float;
-
- uniform sampler2D img;
- // its more direct to do 3 separate channels...
- varying vec2 texCoord;
- void main(){
-
- gl_FragColor =texture2D(img, texCoord);
- }`,
- framebuffer: regl.prop("target"),
- attributes: {
- pos: [0, 0, 1, 0, 1, 1, 0, 1],
- },
- depth: {
- enable: false,
- },
- uniforms: {
- box: regl.prop("box"),
- view: regl.prop("view"),
- img: regl.prop("img"),
- },
- blend: {
- enable: true,
- func: {
- src: "src alpha",
- dst: "one minus src alpha",
- },
- },
- count: 4,
- primitive: "triangle fan",
- // ... more!
- });
- return cmd;
-}
+import type { vec2, vec4 } from '@alleninstitute/vis-geometry';
+import REGL, { type Framebuffer2D } from 'regl';
+
+type Props = {
+ target: Framebuffer2D | null;
+ box: vec4;
+ view: vec4;
+ // viewport: REGL.BoundingBox;
+ img: REGL.Texture2D | REGL.Framebuffer2D;
+};
+export function buildImageRenderer(regl: REGL.Regl) {
+ const cmd = regl<
+ { view: vec4; box: vec4; img: REGL.Texture2D | REGL.Framebuffer2D },
+ { pos: REGL.BufferData },
+ Props
+ >({
+ vert: ` precision highp float;
+ attribute vec2 pos;
+
+ uniform vec4 view;
+ uniform vec4 box;
+ varying vec2 texCoord;
+
+ void main(){
+ vec2 tileSize = box.zw-box.xy;
+ texCoord = pos;
+ vec2 obj = (pos.xy*tileSize+box.xy);
+ vec2 p = (obj-view.xy)/(view.zw-view.xy);
+ // now, to clip space
+ p = (p*2.0)-1.0;
+ gl_Position = vec4(p.x,p.y,0.0,1.0);
+ }`,
+ frag: `
+ precision highp float;
+
+ uniform sampler2D img;
+ // its more direct to do 3 separate channels...
+ varying vec2 texCoord;
+ void main(){
+
+ gl_FragColor =texture2D(img, texCoord);
+ }`,
+ framebuffer: regl.prop('target'),
+ attributes: {
+ pos: [0, 0, 1, 0, 1, 1, 0, 1],
+ },
+ depth: {
+ enable: false,
+ },
+ uniforms: {
+ box: regl.prop('box'),
+ view: regl.prop('view'),
+ img: regl.prop('img'),
+ },
+ blend: {
+ enable: true,
+ func: {
+ src: 'src alpha',
+ dst: 'one minus src alpha',
+ },
+ },
+ count: 4,
+ primitive: 'triangle fan',
+ // ... more!
+ });
+ return cmd;
+}
diff --git a/apps/omezarr-viewer/src/slice-renderer.ts b/apps/omezarr-viewer/src/slice-renderer.ts
index 91473d0..7575c04 100644
--- a/apps/omezarr-viewer/src/slice-renderer.ts
+++ b/apps/omezarr-viewer/src/slice-renderer.ts
@@ -1,255 +1,250 @@
-import REGL from "regl";
-import {
- type ZarrDataset,
- type ZarrRequest,
- getSlice,
- indexOfDimension,
- pickBestScale,
- sizeInUnits,
- planeSizeInVoxels,
-} from "Common/loaders/ome-zarr/zarr-data";;
-import { Box2D, type Interval, Vec2, type box2D, type vec2, type vec4 } from "@alleninstitute/vis-geometry";
-import type { Camera } from "./camera";
-
-type Props = {
- tile: vec4;
- view: vec4;
- gamut: vec2;
- viewport: REGL.BoundingBox;
- img: REGL.Texture2D;
- rot: number;
- target: REGL.Framebuffer2D | null;
-};
-export function buildVolumeSliceRenderer(regl: REGL.Regl) {
- const cmd = regl<
- { view: vec4; tile: vec4; img: REGL.Texture2D; gamut: vec2; rot: number },
- { pos: REGL.BufferData },
- Props
- >({
- vert: ` precision highp float;
- attribute vec2 pos;
-
- uniform vec4 view;
- uniform vec4 tile;
- uniform float rot;
- varying vec2 texCoord;
-
- vec2 rotateObj(vec2 obj, float radians){
- return obj;
- // mat2 R = mat2(
- // vec2(cos(radians),-sin(radians)),
- // vec2(-sin(radians),cos(radians))
- // );
- // return R*obj;
- }
- vec2 rotateTextureCoordinates(vec2 tx, float radians){
- vec2 xy = tx-vec2(0.5,0.5);
- mat2 R = mat2(
- vec2(cos(radians),-sin(radians)),
- vec2(-sin(radians),cos(radians))
- );
- return ((R*xy)+vec2(0.5,0.5));
- }
- void main(){
- vec2 tileSize = (tile.zw-tile.xy);
- texCoord = rotateTextureCoordinates(pos,rot);
- vec2 obj = rotateObj((pos.xy*tileSize+tile.xy),rot);
- vec2 p = (obj-view.xy)/(view.zw-view.xy);
- // now, to clip space
- p = (p*2.0)-1.0;
-
- gl_Position = vec4(p.x,p.y,0.0,1.0);
- }`,
- frag: `
- precision highp float;
- uniform sampler2D img;
- uniform vec2 gamut;
- varying vec2 texCoord;
- void main(){
- float span = gamut.y-gamut.x;
- float lum = texture2D(img, texCoord).r/span-gamut.x;
- gl_FragColor = vec4(lum,lum,lum, 1.0);
- }`,
- attributes: {
- pos: [0, 0, 1, 0, 1, 1, 0, 1],
- },
- uniforms: {
- rot: regl.prop("rot"),
- tile: regl.prop("tile"),
- view: regl.prop("view"),
- img: regl.prop("img"),
- gamut: regl.prop("gamut"),
- },
- depth: {
- enable: false,
- },
- framebuffer: regl.prop("target"),
- count: 4,
- // viewport: regl.prop("viewport"),
- primitive: "triangle fan",
- // ... more!
- });
-
- return (item: VoxelTile, settings: VoxelSliceRenderSettings, tasks: Record) => {
- const { view, viewport, gamut, target } = settings;
- const { bounds } = item;
- const img = tasks[LUMINANCE];
- if (!img || !('type' in img && img.type === 'texture2D')) return; // we cant render if the data for the positions is missing!
- cmd({
- view: [...view.minCorner, ...view.maxCorner],
- tile: [...bounds.minCorner, ...bounds.maxCorner],
- // viewport,
- gamut: [gamut.min, gamut.max],
- img: img.data,
- rot: settings.rotation,
- target,
- });
- };
-}
-type Bfr = { type: 'texture2D', data: REGL.Texture2D };
-
-type Tile = { bounds: box2D };
-export type VoxelSliceRenderSettings = {
- regl: REGL.Regl;
- target: REGL.Framebuffer2D | null;
- dataset: ZarrDataset;
- view: box2D;
- gamut: Interval;
- rotation: number;
- viewport: REGL.BoundingBox;
-};
-export type AxisAlignedPlane = "xy" | "yz" | "xz";
-export type VoxelTile = {
- plane: AxisAlignedPlane;
- bounds: box2D; // in voxels, in the plane
- planeIndex: number;
- layerIndex: number;
- // time and channel are always = 0, for now
-};
-
-function toZarrRequest(tile: VoxelTile): ZarrRequest {
- const { plane, planeIndex, bounds } = tile;
- const { minCorner: min, maxCorner: max } = bounds;
- const u = { min: min[0], max: max[0] };
- const v = { min: min[1], max: max[1] };
- switch (plane) {
- case "xy":
- return {
- x: u,
- y: v,
- t: 0,
- c: 0,
- z: planeIndex,
- };
- case "xz":
- return {
- x: u,
- z: v,
- t: 0,
- c: 0,
- y: planeIndex,
- };
- case "yz":
- return {
- y: u,
- z: v,
- t: 0,
- c: 0,
- x: planeIndex,
- };
- }
-}
-export function cacheKeyFactory(col: string, item: VoxelTile, settings: VoxelSliceRenderSettings) {
- return `${JSON.stringify(item)}_${col}`;
-}
-const LUMINANCE = "luminance";
-export function requestsForTile(tile: VoxelTile, settings: VoxelSliceRenderSettings, signal?: AbortSignal) {
- const { dataset, regl } = settings;
-
- return {
- luminance: async () => {
- // console.log("req: ", tile);
- const vxl = await getSlice(dataset, toZarrRequest(tile), tile.layerIndex);
- // TODO: cancel?
- const { shape, buffer } = vxl;
- // upload the data to a webgl texture
- // draw that texture to the screen with our command
- // console.log("upload new tile: ", cacheKeyFactory("lum", tile, settings));
- const tex = regl.texture({
- data: new Float32Array(buffer.flatten()),
- width: shape[1],
- height: shape[0], // TODO this swap is sus
- format: "luminance",
- });
- return { type: 'texture2D', data: tex };
- },
- };
-}
-
-function getAllTiles(idealTilePx: vec2, layerSize: vec2) {
- // return the set of all our "tiles" of this layer, given the tilePx size
- const tiles: box2D[] = [];
- for (let x = 0; x < layerSize[0]; x += idealTilePx[0]) {
- for (let y = 0; y < layerSize[1]; y += idealTilePx[1]) {
- const xy: vec2 = [x, y];
- tiles.push(Box2D.create(xy, Vec2.min(Vec2.add(xy, idealTilePx), layerSize)));
- }
- }
- return tiles;
-}
-const uvTable = {
- xy: { u: "x", v: "y" },
- xz: { u: "x", v: "z" },
- yz: { u: "y", v: "z" },
-} as const;
-const sliceDimension = {
- xy: "z",
- xz: "y",
- yz: "x",
-} as const;
-
-export function getVisibleTiles(
- camera: Camera,
- plane: AxisAlignedPlane,
- sliceParam: number,
- dataset: ZarrDataset
-): { layer: number; view: box2D; tiles: VoxelTile[] } {
- const { axes, datasets } = dataset.multiscales[0];
- const sliceSize = sizeInUnits(uvTable[plane], axes, datasets[0])!;
-
- const zIndex = indexOfDimension(axes, sliceDimension[plane]);
- const thingy = pickBestScale(
- dataset,
- uvTable[plane],
- camera.view,
- camera.screen
- );
- const thickness = thingy.shape[zIndex];
- const planeIndex = Math.floor(thickness * sliceParam);
- // TODO: open the array, look at its chunks, use that size for the size of the tiles I request!
- const layerIndex = dataset.multiscales[0].datasets.indexOf(thingy);
- const size = planeSizeInVoxels(uvTable[plane], dataset.multiscales[0].axes, thingy);
- const realSize = sizeInUnits(uvTable[plane], dataset.multiscales[0].axes, thingy);
- if (!size || !realSize) return { layer: layerIndex, view: Box2D.create([0, 0], [1, 1]), tiles: [] };
- const scale = Vec2.div(realSize, size);
- // to go from a voxel-box to a real-box (easier than you think, as both have an origin at 0,0, because we only support scale...)
- const vxlToReal = (vxl: box2D) => Box2D.scale(vxl, scale);
- const realToVxl = (real: box2D) => Box2D.scale(real, Vec2.div(size, realSize));
-
- // find the tiles, in voxels, to request...
- const allTiles = getAllTiles([256, 256], size);
- const inView = allTiles.filter((tile) => !!Box2D.intersection(camera.view, vxlToReal(tile)));
- // camera.view is in a made up dataspace, where 1=height of the current dataset
- // thus, we have to convert it into a voxel-space camera for intersections
- const voxelView = realToVxl(camera.view);
- return {
- layer: layerIndex,
- view: voxelView,
- tiles: inView.map((uv) => ({
- plane,
- bounds: uv,
- planeIndex,
- layerIndex,
- })),
- };
-}
+import REGL from 'regl';
+import {
+ type ZarrDataset,
+ type ZarrRequest,
+ getSlice,
+ indexOfDimension,
+ pickBestScale,
+ sizeInUnits,
+ planeSizeInVoxels,
+} from 'Common/loaders/ome-zarr/zarr-data';
+import { Box2D, type Interval, Vec2, type box2D, type vec2, type vec4 } from '@alleninstitute/vis-geometry';
+import type { Camera } from './camera';
+
+type Props = {
+ tile: vec4;
+ view: vec4;
+ gamut: vec2;
+ viewport: REGL.BoundingBox;
+ img: REGL.Texture2D;
+ rot: number;
+ target: REGL.Framebuffer2D | null;
+};
+export function buildVolumeSliceRenderer(regl: REGL.Regl) {
+ const cmd = regl<
+ { view: vec4; tile: vec4; img: REGL.Texture2D; gamut: vec2; rot: number },
+ { pos: REGL.BufferData },
+ Props
+ >({
+ vert: ` precision highp float;
+ attribute vec2 pos;
+
+ uniform vec4 view;
+ uniform vec4 tile;
+ uniform float rot;
+ varying vec2 texCoord;
+
+ vec2 rotateObj(vec2 obj, float radians){
+ return obj;
+ // mat2 R = mat2(
+ // vec2(cos(radians),-sin(radians)),
+ // vec2(-sin(radians),cos(radians))
+ // );
+ // return R*obj;
+ }
+ vec2 rotateTextureCoordinates(vec2 tx, float radians){
+ vec2 xy = tx-vec2(0.5,0.5);
+ mat2 R = mat2(
+ vec2(cos(radians),-sin(radians)),
+ vec2(-sin(radians),cos(radians))
+ );
+ return ((R*xy)+vec2(0.5,0.5));
+ }
+ void main(){
+ vec2 tileSize = (tile.zw-tile.xy);
+ texCoord = rotateTextureCoordinates(pos,rot);
+ vec2 obj = rotateObj((pos.xy*tileSize+tile.xy),rot);
+ vec2 p = (obj-view.xy)/(view.zw-view.xy);
+ // now, to clip space
+ p = (p*2.0)-1.0;
+
+ gl_Position = vec4(p.x,p.y,0.0,1.0);
+ }`,
+ frag: `
+ precision highp float;
+ uniform sampler2D img;
+ uniform vec2 gamut;
+ varying vec2 texCoord;
+ void main(){
+ float span = gamut.y-gamut.x;
+ float lum = texture2D(img, texCoord).r/span-gamut.x;
+ gl_FragColor = vec4(lum,lum,lum, 1.0);
+ }`,
+ attributes: {
+ pos: [0, 0, 1, 0, 1, 1, 0, 1],
+ },
+ uniforms: {
+ rot: regl.prop('rot'),
+ tile: regl.prop('tile'),
+ view: regl.prop('view'),
+ img: regl.prop('img'),
+ gamut: regl.prop('gamut'),
+ },
+ depth: {
+ enable: false,
+ },
+ framebuffer: regl.prop('target'),
+ count: 4,
+ // viewport: regl.prop("viewport"),
+ primitive: 'triangle fan',
+ // ... more!
+ });
+
+ return (item: VoxelTile, settings: VoxelSliceRenderSettings, tasks: Record) => {
+ const { view, viewport, gamut, target } = settings;
+ const { bounds } = item;
+ const img = tasks[LUMINANCE];
+ if (!img || !('type' in img && img.type === 'texture2D')) return; // we cant render if the data for the positions is missing!
+ cmd({
+ view: [...view.minCorner, ...view.maxCorner],
+ tile: [...bounds.minCorner, ...bounds.maxCorner],
+ // viewport,
+ gamut: [gamut.min, gamut.max],
+ img: img.data,
+ rot: settings.rotation,
+ target,
+ });
+ };
+}
+type Bfr = { type: 'texture2D'; data: REGL.Texture2D };
+
+type Tile = { bounds: box2D };
+export type VoxelSliceRenderSettings = {
+ regl: REGL.Regl;
+ target: REGL.Framebuffer2D | null;
+ dataset: ZarrDataset;
+ view: box2D;
+ gamut: Interval;
+ rotation: number;
+ viewport: REGL.BoundingBox;
+};
+export type AxisAlignedPlane = 'xy' | 'yz' | 'xz';
+export type VoxelTile = {
+ plane: AxisAlignedPlane;
+ bounds: box2D; // in voxels, in the plane
+ planeIndex: number;
+ layerIndex: number;
+ // time and channel are always = 0, for now
+};
+
+function toZarrRequest(tile: VoxelTile): ZarrRequest {
+ const { plane, planeIndex, bounds } = tile;
+ const { minCorner: min, maxCorner: max } = bounds;
+ const u = { min: min[0], max: max[0] };
+ const v = { min: min[1], max: max[1] };
+ switch (plane) {
+ case 'xy':
+ return {
+ x: u,
+ y: v,
+ t: 0,
+ c: 0,
+ z: planeIndex,
+ };
+ case 'xz':
+ return {
+ x: u,
+ z: v,
+ t: 0,
+ c: 0,
+ y: planeIndex,
+ };
+ case 'yz':
+ return {
+ y: u,
+ z: v,
+ t: 0,
+ c: 0,
+ x: planeIndex,
+ };
+ }
+}
+export function cacheKeyFactory(col: string, item: VoxelTile, settings: VoxelSliceRenderSettings) {
+ return `${JSON.stringify(item)}_${col}`;
+}
+const LUMINANCE = 'luminance';
+export function requestsForTile(tile: VoxelTile, settings: VoxelSliceRenderSettings, signal?: AbortSignal) {
+ const { dataset, regl } = settings;
+
+ return {
+ luminance: async () => {
+ // console.log("req: ", tile);
+ const vxl = await getSlice(dataset, toZarrRequest(tile), tile.layerIndex);
+ // TODO: cancel?
+ const { shape, buffer } = vxl;
+ // upload the data to a webgl texture
+ // draw that texture to the screen with our command
+ // console.log("upload new tile: ", cacheKeyFactory("lum", tile, settings));
+ const tex = regl.texture({
+ data: new Float32Array(buffer.flatten()),
+ width: shape[1],
+ height: shape[0], // TODO this swap is sus
+ format: 'luminance',
+ });
+ return { type: 'texture2D', data: tex };
+ },
+ };
+}
+
+function getAllTiles(idealTilePx: vec2, layerSize: vec2) {
+ // return the set of all our "tiles" of this layer, given the tilePx size
+ const tiles: box2D[] = [];
+ for (let x = 0; x < layerSize[0]; x += idealTilePx[0]) {
+ for (let y = 0; y < layerSize[1]; y += idealTilePx[1]) {
+ const xy: vec2 = [x, y];
+ tiles.push(Box2D.create(xy, Vec2.min(Vec2.add(xy, idealTilePx), layerSize)));
+ }
+ }
+ return tiles;
+}
+const uvTable = {
+ xy: { u: 'x', v: 'y' },
+ xz: { u: 'x', v: 'z' },
+ yz: { u: 'y', v: 'z' },
+} as const;
+const sliceDimension = {
+ xy: 'z',
+ xz: 'y',
+ yz: 'x',
+} as const;
+
+export function getVisibleTiles(
+ camera: Camera,
+ plane: AxisAlignedPlane,
+ sliceParam: number,
+ dataset: ZarrDataset
+): { layer: number; view: box2D; tiles: VoxelTile[] } {
+ const { axes, datasets } = dataset.multiscales[0];
+ const sliceSize = sizeInUnits(uvTable[plane], axes, datasets[0])!;
+
+ const zIndex = indexOfDimension(axes, sliceDimension[plane]);
+ const thingy = pickBestScale(dataset, uvTable[plane], camera.view, camera.screen);
+ const thickness = thingy.shape[zIndex];
+ const planeIndex = Math.floor(thickness * sliceParam);
+ // TODO: open the array, look at its chunks, use that size for the size of the tiles I request!
+ const layerIndex = dataset.multiscales[0].datasets.indexOf(thingy);
+ const size = planeSizeInVoxels(uvTable[plane], dataset.multiscales[0].axes, thingy);
+ const realSize = sizeInUnits(uvTable[plane], dataset.multiscales[0].axes, thingy);
+ if (!size || !realSize) return { layer: layerIndex, view: Box2D.create([0, 0], [1, 1]), tiles: [] };
+ const scale = Vec2.div(realSize, size);
+ // to go from a voxel-box to a real-box (easier than you think, as both have an origin at 0,0, because we only support scale...)
+ const vxlToReal = (vxl: box2D) => Box2D.scale(vxl, scale);
+ const realToVxl = (real: box2D) => Box2D.scale(real, Vec2.div(size, realSize));
+
+ // find the tiles, in voxels, to request...
+ const allTiles = getAllTiles([256, 256], size);
+ const inView = allTiles.filter((tile) => !!Box2D.intersection(camera.view, vxlToReal(tile)));
+ // camera.view is in a made up dataspace, where 1=height of the current dataset
+ // thus, we have to convert it into a voxel-space camera for intersections
+ const voxelView = realToVxl(camera.view);
+ return {
+ layer: layerIndex,
+ view: voxelView,
+ tiles: inView.map((uv) => ({
+ plane,
+ bounds: uv,
+ planeIndex,
+ layerIndex,
+ })),
+ };
+}
diff --git a/apps/omezarr-viewer/src/tissuecyte.ts b/apps/omezarr-viewer/src/tissuecyte.ts
index a4057f0..e4d3179 100644
--- a/apps/omezarr-viewer/src/tissuecyte.ts
+++ b/apps/omezarr-viewer/src/tissuecyte.ts
@@ -1,482 +1,499 @@
// I am the scatterplot demo //
-import { ImGui, ImGui_Impl } from "@zhobo63/imgui-ts";
-import REGL from "regl";
+import { ImGui, ImGui_Impl } from '@zhobo63/imgui-ts';
+import REGL from 'regl';
import {
- type ZarrDataset,
- explain,
- getSlice,
- indexOfDimension,
- load,
- pickBestScale,
- sizeInUnits,
- planeSizeInVoxels,
-} from "Common/loaders/ome-zarr/zarr-data";
-import { AsyncDataCache, type FrameLifecycle, beginLongRunningFrame } from "@alleninstitute/vis-scatterbrain";
+ type ZarrDataset,
+ explain,
+ getSlice,
+ indexOfDimension,
+ load,
+ pickBestScale,
+ sizeInUnits,
+ planeSizeInVoxels,
+} from 'Common/loaders/ome-zarr/zarr-data';
+import { AsyncDataCache, type FrameLifecycle, beginLongRunningFrame } from '@alleninstitute/vis-scatterbrain';
-import { Box2D, type Interval, Vec2, type box2D, type vec2 } from "@alleninstitute/vis-geometry";
-import type { Camera } from "./camera";
-import { buildImageRenderer } from "./image-renderer";
-import { ImVec2, ImVec4 } from "@zhobo63/imgui-ts/src/imgui";
-import { colorMapWidget } from "./components/color-map";
-import { initDrawableInterface } from "./annotation/path";
+import { Box2D, type Interval, Vec2, type box2D, type vec2 } from '@alleninstitute/vis-geometry';
+import type { Camera } from './camera';
+import { buildImageRenderer } from './image-renderer';
+import { ImVec2, ImVec4 } from '@zhobo63/imgui-ts/src/imgui';
+import { colorMapWidget } from './components/color-map';
+import { initDrawableInterface } from './annotation/path';
import {
- type AxisAlignedPlane,
- type VoxelSliceRenderSettings,
- type VoxelTile,
- buildVolumeSliceRenderer,
- cacheKeyFactory,
- getVisibleTiles,
- requestsForTile,
-} from "./slice-renderer";
+ type AxisAlignedPlane,
+ type VoxelSliceRenderSettings,
+ type VoxelTile,
+ buildVolumeSliceRenderer,
+ cacheKeyFactory,
+ getVisibleTiles,
+ requestsForTile,
+} from './slice-renderer';
const creepy =
- "https://aind-open-data.s3.amazonaws.com/SmartSPIM_644106_2022-12-09_12-12-39_stitched_2022-12-16_16-55-11/processed/OMEZarr/Ex_488_Em_525.zarr";
-const tissuecyte = "https://tissuecyte-visualizations.s3.amazonaws.com/data/230105/tissuecyte/1111175209/green/";
+ 'https://aind-open-data.s3.amazonaws.com/SmartSPIM_644106_2022-12-09_12-12-39_stitched_2022-12-16_16-55-11/processed/OMEZarr/Ex_488_Em_525.zarr';
+const tissuecyte = 'https://tissuecyte-visualizations.s3.amazonaws.com/data/230105/tissuecyte/1111175209/green/';
// const versa = "https://neuroglancer-vis-prototype.s3.amazonaws.com/VERSA/scratch/0500408166/";
// const b = "https://neuroglancer-vis-prototype.s3.amazonaws.com/VERSA/ome_zarr/20231207.1/1282139033/";
// const scott = "https://neuroglancer-vis-prototype.s3.amazonaws.com/VERSA/ome_zarr/20231204/1197986710/";
const file = tissuecyte;
-type Channel = "R" | "G" | "B"; // we can support 3 visual channels at once
+type Channel = 'R' | 'G' | 'B'; // we can support 3 visual channels at once
type ChannelColorSettings = {
- gamut: Interval;
- index: number;
+ gamut: Interval;
+ index: number;
};
class TissuecyteDemo {
- mouse: "up" | "down";
- mousePos: vec2;
- camera: Camera;
- channels: Record;
- plane: AxisAlignedPlane;
- sliceParameter: number;
- canvas: HTMLCanvasElement;
- curFrame: FrameLifecycle | null;
- rotation: number;
- cache: AsyncDataCache;
- regl: REGL.Regl;
- dataset: ZarrDataset;
- screenRenderer: ReturnType;
- renderer: ReturnType;
- screenBuffer: { bounds: box2D; fbo: REGL.Framebuffer2D };
- datasets: string[];
- constructor(
- canvas: HTMLCanvasElement,
- dataset: ZarrDataset,
- regl: REGL.Regl,
- cache: AsyncDataCache,
- urls: string[]
- ) {
- const [w, h] = [canvas.clientWidth, canvas.clientHeight];
- this.datasets = urls;
+ mouse: 'up' | 'down';
+ mousePos: vec2;
+ camera: Camera;
+ channels: Record;
+ plane: AxisAlignedPlane;
+ sliceParameter: number;
+ canvas: HTMLCanvasElement;
+ curFrame: FrameLifecycle | null;
+ rotation: number;
+ cache: AsyncDataCache;
+ regl: REGL.Regl;
+ dataset: ZarrDataset;
+ screenRenderer: ReturnType;
+ renderer: ReturnType;
+ screenBuffer: { bounds: box2D; fbo: REGL.Framebuffer2D };
+ datasets: string[];
+ constructor(
+ canvas: HTMLCanvasElement,
+ dataset: ZarrDataset,
+ regl: REGL.Regl,
+ cache: AsyncDataCache,
+ urls: string[]
+ ) {
+ const [w, h] = [canvas.clientWidth, canvas.clientHeight];
+ this.datasets = urls;
- const sliceSize = sizeInUnits({ u: "x", v: "y" }, dataset.multiscales[0].axes, dataset.multiscales[0].datasets[0])!;
- this.camera = {
- view: Box2D.create([0, 0], [(sliceSize[1] * w) / h, sliceSize[1]]),
- screen: [w, h],
- };
- this.screenBuffer = { bounds: this.camera.view, fbo: regl.framebuffer(w, h) };
- this.dataset = dataset;
- this.regl = regl;
- this.plane = "yz";
- this.mouse = "up";
- this.cache = cache;
- this.sliceParameter = 0.5;
- this.mousePos = [0, 0];
- this.channels = {
- R: {
- gamut: { min: 0, max: 2500 },
- index: 0,
- },
- // G: {
- // gamut: { min: 0, max: 0.21 },
- // index: 1,
- // },
- // B: {
- // gamut: { min: 0, max: 0.21 },
- // index: 2,
- // },
- };
- this.canvas = canvas;
- this.curFrame = null;
- this.rotation = (3 * Math.PI) / 2;
- this.renderer = buildVolumeSliceRenderer(regl);
- this.screenRenderer = buildImageRenderer(regl);
- const loop = () => {
- this.refreshScreen();
- window.requestAnimationFrame(loop);
- };
- window.requestAnimationFrame(loop);
- }
- setupEventHandlers() {
- const canvas = this.canvas;
- }
-
- private upsideDown(v: box2D) {
- const { minCorner, maxCorner } = v;
- return Box2D.create([minCorner[0], maxCorner[1]], [maxCorner[0], minCorner[1]]);
- }
- private renderFrame() {
- const { camera, plane, sliceParameter, dataset, cache, regl, channels, renderer } = this;
- const { layer, view, tiles } = getVisibleTiles(camera, plane, sliceParameter, dataset);
- // erase our buffer that holds the render'd dataset image - which lets the UI
- // re-render itself independantly
- regl.clear({ color: [0, 0, 0, 0], depth: 1, framebuffer: this.screenBuffer.fbo });
-
- // get the lowest-resolution view of the current slice - the idea being that we keep
- // it cached, and always draw it UNDER the actual layer we want to see, based on our zoom.
- // this prevents a flickering black frame when we zoom in to a new, higher resolution layer
- const {
- layer: baseLayer,
- view: baseView,
- tiles: baseTiles,
- } = getVisibleTiles({ ...camera, screen: [1, 1] }, plane, sliceParameter, dataset);
- if (layer === baseLayer) {
- this.curFrame = this.renderFrameHelper(baseView, baseTiles);
- // if the layer we WANT is actually the lowest res layer, then we're done here and now!
- return;
+ const sliceSize = sizeInUnits(
+ { u: 'x', v: 'y' },
+ dataset.multiscales[0].axes,
+ dataset.multiscales[0].datasets[0]
+ )!;
+ this.camera = {
+ view: Box2D.create([0, 0], [(sliceSize[1] * w) / h, sliceSize[1]]),
+ screen: [w, h],
+ };
+ this.screenBuffer = { bounds: this.camera.view, fbo: regl.framebuffer(w, h) };
+ this.dataset = dataset;
+ this.regl = regl;
+ this.plane = 'yz';
+ this.mouse = 'up';
+ this.cache = cache;
+ this.sliceParameter = 0.5;
+ this.mousePos = [0, 0];
+ this.channels = {
+ R: {
+ gamut: { min: 0, max: 2500 },
+ index: 0,
+ },
+ // G: {
+ // gamut: { min: 0, max: 0.21 },
+ // index: 1,
+ // },
+ // B: {
+ // gamut: { min: 0, max: 0.21 },
+ // index: 2,
+ // },
+ };
+ this.canvas = canvas;
+ this.curFrame = null;
+ this.rotation = (3 * Math.PI) / 2;
+ this.renderer = buildVolumeSliceRenderer(regl);
+ this.screenRenderer = buildImageRenderer(regl);
+ const loop = () => {
+ this.refreshScreen();
+ window.requestAnimationFrame(loop);
+ };
+ window.requestAnimationFrame(loop);
+ }
+ setupEventHandlers() {
+ const canvas = this.canvas;
}
- const baseSettings = {
- view: baseView,
- dataset,
- regl,
- target: this.screenBuffer.fbo,
- viewport: {
- x: 0,
- y: 0,
- width: this.canvas.clientWidth,
- height: this.canvas.clientHeight,
- },
- rotation: this.rotation,
- gamut: this.channels.R.gamut,
- // gamut: channels,
- };
- const cached = baseTiles.reduce(
- (count, cur) => (cache.isCached(cacheKeyFactory("luminance", cur, baseSettings)) ? 1 + count : count),
- 0
- );
- if (cached === 0) {
- this.curFrame = this.renderFrameHelper(view, tiles);
- return;
+ private upsideDown(v: box2D) {
+ const { minCorner, maxCorner } = v;
+ return Box2D.create([minCorner[0], maxCorner[1]], [maxCorner[0], minCorner[1]]);
}
- const frame = beginLongRunningFrame(
- 3,
- 33,
- baseTiles,
- cache,
- baseSettings,
- requestsForTile,
- renderer,
- (event) => {
- switch (event.status) {
- case "error":
- throw event.error; // error boundary might catch this
- case "progress":
- break;
- case "finished_synchronously":
- case "finished":
- console.log("finished base-layer... start real frame!");
- this.curFrame = this.renderFrameHelper(view, tiles);
- break;
- case "begun":
- break;
- case "cancelled":
- this.curFrame = this.renderFrameHelper(view, tiles);
- break;
- default:
+ private renderFrame() {
+ const { camera, plane, sliceParameter, dataset, cache, regl, channels, renderer } = this;
+ const { layer, view, tiles } = getVisibleTiles(camera, plane, sliceParameter, dataset);
+ // erase our buffer that holds the render'd dataset image - which lets the UI
+ // re-render itself independantly
+ regl.clear({ color: [0, 0, 0, 0], depth: 1, framebuffer: this.screenBuffer.fbo });
+
+ // get the lowest-resolution view of the current slice - the idea being that we keep
+ // it cached, and always draw it UNDER the actual layer we want to see, based on our zoom.
+ // this prevents a flickering black frame when we zoom in to a new, higher resolution layer
+ const {
+ layer: baseLayer,
+ view: baseView,
+ tiles: baseTiles,
+ } = getVisibleTiles({ ...camera, screen: [1, 1] }, plane, sliceParameter, dataset);
+ if (layer === baseLayer) {
+ this.curFrame = this.renderFrameHelper(baseView, baseTiles);
+ // if the layer we WANT is actually the lowest res layer, then we're done here and now!
+ return;
}
- },
- cacheKeyFactory
- );
- frame.cancelFrame();
- }
- // not my fav thing to do - but renderFrame and renderFrame helper are tightly linked
- // to accomplish our smoke&mirrors to avoid flickering as tiles load in -
- // the both make assumptions about state, and the contents of buffers. do not
- // call either of them!
- private renderFrameHelper(view: box2D, visibleTiles: VoxelTile[]) {
- const { camera, dataset, cache, regl, channels, renderer } = this;
- this.screenBuffer.bounds = camera.view;
- regl.clear({ depth: 1, framebuffer: this.screenBuffer.fbo });
- // const gamut = {
- // R: channels.R.gamut,
- // G: channels.G.gamut,
- // B: channels.B.gamut,
- // };
- const frame = beginLongRunningFrame(
- 3,
- 33,
- visibleTiles,
- cache,
- {
- rotation: this.rotation,
- gamut: this.channels.R.gamut,
- view: view,
- dataset,
- regl,
- target: this.screenBuffer.fbo,
- viewport: {
- x: 0,
- y: 0,
- width: this.canvas.clientWidth,
- height: this.canvas.clientHeight,
- },
- // gamut: channels,
- },
- requestsForTile,
- renderer,
- (event) => {
- switch (event.status) {
- case "error":
- throw event.error; // error boundary might catch this
- case "progress":
- this.refreshScreen();
- break;
- case "finished_synchronously":
- case "finished":
- this.curFrame = null;
- this.refreshScreen();
- break;
- case "begun":
- this.refreshScreen();
- break;
- case "cancelled":
- break;
- default:
+ const baseSettings = {
+ view: baseView,
+ dataset,
+ regl,
+ target: this.screenBuffer.fbo,
+ viewport: {
+ x: 0,
+ y: 0,
+ width: this.canvas.clientWidth,
+ height: this.canvas.clientHeight,
+ },
+ rotation: this.rotation,
+ gamut: this.channels.R.gamut,
+ // gamut: channels,
+ };
+
+ const cached = baseTiles.reduce(
+ (count, cur) => (cache.isCached(cacheKeyFactory('luminance', cur, baseSettings)) ? 1 + count : count),
+ 0
+ );
+ if (cached === 0) {
+ this.curFrame = this.renderFrameHelper(view, tiles);
+ return;
}
- },
- cacheKeyFactory
- );
- return frame;
- }
- refreshScreen() {
- const now = performance.now();
- this.regl._refresh();
- this.regl.clear({ depth: 1, color: [0, 0, 0, 1], framebuffer: null });
+ const frame = beginLongRunningFrame(
+ 3,
+ 33,
+ baseTiles,
+ cache,
+ baseSettings,
+ requestsForTile,
+ renderer,
+ (event) => {
+ switch (event.status) {
+ case 'error':
+ throw event.error; // error boundary might catch this
+ case 'progress':
+ break;
+ case 'finished_synchronously':
+ case 'finished':
+ console.log('finished base-layer... start real frame!');
+ this.curFrame = this.renderFrameHelper(view, tiles);
+ break;
+ case 'begun':
+ break;
+ case 'cancelled':
+ this.curFrame = this.renderFrameHelper(view, tiles);
+ break;
+ default:
+ }
+ },
+ cacheKeyFactory
+ );
+ frame.cancelFrame();
+ }
+ // not my fav thing to do - but renderFrame and renderFrame helper are tightly linked
+ // to accomplish our smoke&mirrors to avoid flickering as tiles load in -
+ // the both make assumptions about state, and the contents of buffers. do not
+ // call either of them!
+ private renderFrameHelper(view: box2D, visibleTiles: VoxelTile[]) {
+ const { camera, dataset, cache, regl, channels, renderer } = this;
+ this.screenBuffer.bounds = camera.view;
+ regl.clear({ depth: 1, framebuffer: this.screenBuffer.fbo });
+ // const gamut = {
+ // R: channels.R.gamut,
+ // G: channels.G.gamut,
+ // B: channels.B.gamut,
+ // };
+ const frame = beginLongRunningFrame(
+ 3,
+ 33,
+ visibleTiles,
+ cache,
+ {
+ rotation: this.rotation,
+ gamut: this.channels.R.gamut,
+ view: view,
+ dataset,
+ regl,
+ target: this.screenBuffer.fbo,
+ viewport: {
+ x: 0,
+ y: 0,
+ width: this.canvas.clientWidth,
+ height: this.canvas.clientHeight,
+ },
+ // gamut: channels,
+ },
+ requestsForTile,
+ renderer,
+ (event) => {
+ switch (event.status) {
+ case 'error':
+ throw event.error; // error boundary might catch this
+ case 'progress':
+ this.refreshScreen();
+ break;
+ case 'finished_synchronously':
+ case 'finished':
+ this.curFrame = null;
+ this.refreshScreen();
+ break;
+ case 'begun':
+ this.refreshScreen();
+ break;
+ case 'cancelled':
+ break;
+ default:
+ }
+ },
+ cacheKeyFactory
+ );
+ return frame;
+ }
+ refreshScreen() {
+ const now = performance.now();
+ this.regl._refresh();
+ this.regl.clear({ depth: 1, color: [0, 0, 0, 1], framebuffer: null });
- this.screenRenderer([
- {
- box: Box2D.toFlatArray(this.screenBuffer.bounds),
- img: this.screenBuffer.fbo,
- target: null,
- view: Box2D.toFlatArray(this.upsideDown(this.camera.view)),
- },
- ]);
+ this.screenRenderer([
+ {
+ box: Box2D.toFlatArray(this.screenBuffer.bounds),
+ img: this.screenBuffer.fbo,
+ target: null,
+ view: Box2D.toFlatArray(this.upsideDown(this.camera.view)),
+ },
+ ]);
- this.drawUI(now);
+ this.drawUI(now);
- this.regl._refresh();
- }
+ this.regl._refresh();
+ }
- drawUI(time: number) {
- let drawAgain = false;
- const effects: Array<() => void> = [];
- // imgui wants mutable access to stuff... which is pretty weird - imAccess is nice, but all the vector-style updaters are nasty
- try {
- ImGui_Impl.NewFrame(time);
- ImGui.NewFrame();
- ImGui.Begin("Settings");
- ImGui_Impl.ClearBuffer(new ImVec4(0.2, 0.2, 0.2, 1));
- // ImGui_Impl.ClearBuffer(new ImVec4(0, 0, 0, 0));
- // TODO: count the available channels that we could use for color!
- Object.entries(this.channels).forEach(([channel, settings]) => {
- const result = colorMapWidget(
- channel,
- {
- gamut: settings.gamut,
- color: new ImGui.Vec4(channel === "R" ? 255 : 0, channel === "G" ? 255 : 0, channel === "B" ? 255 : 0, 255),
- useMe: true,
- index: settings.index,
- },
- 3
- );
- if (result.changed) {
- this.channels[channel as Channel].gamut = result.gamut;
- this.channels[channel as Channel].index = result.index;
- drawAgain = true;
- }
- });
- const highlight = new ImVec4(0, 0.25, 0.65, 1.0);
- const regular = new ImVec4(0.2, 0.2, 0.2, 1.0);
- // for (const thumb of this.sliceThumbs) {
- // if (
- // // here we dig deep into the guts of a regl-managed texture... not super safe, and regl's types are not really set up for this:
- // ImGui.ImageButton(
- // // @ts-expect-error
- // thumb?.color[0]?._texture?.texture ?? null,
- // new ImVec2(this.thumbWidth, THUMB_SIZE),
- // new ImVec2(0, 0),
- // new ImVec2(1, 1),
- // // draw a little box around the selected slice:
- // this.sliceIndex === this.sliceThumbs.indexOf(thumb) ? 3 : 0,
- // this.sliceIndex === this.sliceThumbs.indexOf(thumb) ? highlight : regular
- // )
- // ) {
- // drawAgain = true;
- // effects.push(() => this.setSlice(this.sliceThumbs.indexOf(thumb)));
- // }
- // ImGui.SameLine();
- // }
- let p = this.sliceParameter;
- if (
- ImGui.DragFloat(
- "slice",
- (v?: number) => {
- p = v ?? p;
- return p;
- },
- 0.005,
- 0.0,
- 1.0,
- "%4f"
- )
- ) {
- effects.push(() => (this.sliceParameter = p));
- drawAgain = true;
- }
- ImGui.End();
- ImGui.EndFrame();
- ImGui.Render();
+ drawUI(time: number) {
+ let drawAgain = false;
+ const effects: Array<() => void> = [];
+ // imgui wants mutable access to stuff... which is pretty weird - imAccess is nice, but all the vector-style updaters are nasty
+ try {
+ ImGui_Impl.NewFrame(time);
+ ImGui.NewFrame();
+ ImGui.Begin('Settings');
+ ImGui_Impl.ClearBuffer(new ImVec4(0.2, 0.2, 0.2, 1));
+ // ImGui_Impl.ClearBuffer(new ImVec4(0, 0, 0, 0));
+ // TODO: count the available channels that we could use for color!
+ Object.entries(this.channels).forEach(([channel, settings]) => {
+ const result = colorMapWidget(
+ channel,
+ {
+ gamut: settings.gamut,
+ color: new ImGui.Vec4(
+ channel === 'R' ? 255 : 0,
+ channel === 'G' ? 255 : 0,
+ channel === 'B' ? 255 : 0,
+ 255
+ ),
+ useMe: true,
+ index: settings.index,
+ },
+ 3
+ );
+ if (result.changed) {
+ this.channels[channel as Channel].gamut = result.gamut;
+ this.channels[channel as Channel].index = result.index;
+ drawAgain = true;
+ }
+ });
+ const highlight = new ImVec4(0, 0.25, 0.65, 1.0);
+ const regular = new ImVec4(0.2, 0.2, 0.2, 1.0);
+ // for (const thumb of this.sliceThumbs) {
+ // if (
+ // // here we dig deep into the guts of a regl-managed texture... not super safe, and regl's types are not really set up for this:
+ // ImGui.ImageButton(
+ // // @ts-expect-error
+ // thumb?.color[0]?._texture?.texture ?? null,
+ // new ImVec2(this.thumbWidth, THUMB_SIZE),
+ // new ImVec2(0, 0),
+ // new ImVec2(1, 1),
+ // // draw a little box around the selected slice:
+ // this.sliceIndex === this.sliceThumbs.indexOf(thumb) ? 3 : 0,
+ // this.sliceIndex === this.sliceThumbs.indexOf(thumb) ? highlight : regular
+ // )
+ // ) {
+ // drawAgain = true;
+ // effects.push(() => this.setSlice(this.sliceThumbs.indexOf(thumb)));
+ // }
+ // ImGui.SameLine();
+ // }
+ let p = this.sliceParameter;
+ if (
+ ImGui.DragFloat(
+ 'slice',
+ (v?: number) => {
+ p = v ?? p;
+ return p;
+ },
+ 0.005,
+ 0.0,
+ 1.0,
+ '%4f'
+ )
+ ) {
+ effects.push(() => (this.sliceParameter = p));
+ drawAgain = true;
+ }
+ ImGui.End();
+ ImGui.EndFrame();
+ ImGui.Render();
- ImGui_Impl.RenderDrawData(ImGui.GetDrawData());
- effects.forEach((fx) => fx());
- if (drawAgain) {
- window.setTimeout(() => this.rerender(), 5);
- }
- } catch (err) {
- console.warn(err);
+ ImGui_Impl.RenderDrawData(ImGui.GetDrawData());
+ effects.forEach((fx) => fx());
+ if (drawAgain) {
+ window.setTimeout(() => this.rerender(), 5);
+ }
+ } catch (err) {
+ console.warn(err);
+ }
}
- }
- rerender() {
- if (this.curFrame !== null) {
- this.curFrame.cancelFrame();
+ rerender() {
+ if (this.curFrame !== null) {
+ this.curFrame.cancelFrame();
+ }
+ this.renderFrame();
+ }
+ mouseButton(click: 'up' | 'down') {
+ this.mouse = click;
}
- this.renderFrame();
- }
- mouseButton(click: "up" | "down") {
- this.mouse = click;
- }
- mouseMove(delta: vec2) {
- if (this.mouse === "down") {
- // drag the view
- const { screen, view } = this.camera;
- const p = Vec2.div(delta, [this.canvas.clientWidth, this.canvas.clientHeight]);
- const c = Vec2.mul(p, Box2D.size(view));
- this.camera = { view: Box2D.translate(view, c), screen };
- this.rerender();
+ mouseMove(delta: vec2) {
+ if (this.mouse === 'down') {
+ // drag the view
+ const { screen, view } = this.camera;
+ const p = Vec2.div(delta, [this.canvas.clientWidth, this.canvas.clientHeight]);
+ const c = Vec2.mul(p, Box2D.size(view));
+ this.camera = { view: Box2D.translate(view, c), screen };
+ this.rerender();
+ }
+ this.mousePos = Vec2.add(this.mousePos, delta);
+ }
+ changeSlice(delta: number) {
+ this.sliceParameter += delta;
+ this.rerender();
}
- this.mousePos = Vec2.add(this.mousePos, delta);
- }
- changeSlice(delta: number) {
- this.sliceParameter += delta;
- this.rerender();
- }
- changeGamut(delta: number) {
- this.channels.R.gamut = { min: this.channels.R.gamut.min, max: this.channels.R.gamut.max * delta };
- this.rerender();
- }
- zoom(scale: number) {
- const { view, screen } = this.camera;
- const m = Box2D.midpoint(view);
- this.camera = {
- view: Box2D.translate(Box2D.scale(Box2D.translate(view, Vec2.scale(m, -1)), [scale, scale]), m),
- screen,
- };
- this.rerender();
- }
- nextAxis() {
- this.plane = this.plane == "xy" ? "xz" : this.plane === "xz" ? "yz" : "xy";
- this.rerender();
- }
- rotateTiles() {
- this.rotation += Math.PI / 2;
- this.rerender();
- }
+ changeGamut(delta: number) {
+ this.channels.R.gamut = { min: this.channels.R.gamut.min, max: this.channels.R.gamut.max * delta };
+ this.rerender();
+ }
+ zoom(scale: number) {
+ const { view, screen } = this.camera;
+ const m = Box2D.midpoint(view);
+ this.camera = {
+ view: Box2D.translate(Box2D.scale(Box2D.translate(view, Vec2.scale(m, -1)), [scale, scale]), m),
+ screen,
+ };
+ this.rerender();
+ }
+ nextAxis() {
+ this.plane = this.plane == 'xy' ? 'xz' : this.plane === 'xz' ? 'yz' : 'xy';
+ this.rerender();
+ }
+ rotateTiles() {
+ this.rotation += Math.PI / 2;
+ this.rerender();
+ }
}
function setupEventHandlers(canvas: HTMLCanvasElement, demo: TissuecyteDemo) {
- canvas.onmousedown = (e: MouseEvent) => {
- if (ImGui.GetIO().WantCaptureMouse) return;
- demo.mouseButton("down");
- };
- canvas.onmouseup = (e: MouseEvent) => {
- if (ImGui.GetIO().WantCaptureMouse) return;
- demo.mouseButton("up");
- };
- canvas.onmousemove = (e: MouseEvent) => {
- if (ImGui.GetIO().WantCaptureMouse) return;
- // account for gl-origin vs. screen origin:
- demo.mouseMove([-e.movementX, -e.movementY]);
- };
- canvas.onwheel = (e: WheelEvent) => {
- if (e.shiftKey) {
- demo.changeGamut(e.deltaY > 0 ? 1.1 : 0.9);
- } else if (e.altKey) {
- demo.changeSlice(e.deltaY > 0 ? 0.01 : -0.01);
- } else {
- demo.zoom(e.deltaY > 0 ? 1.1 : 0.9);
- }
- };
- canvas.onkeydown = (e: KeyboardEvent) => {
- switch (e.key) {
- case "a":
- demo.nextAxis();
- break;
- case "r":
- demo.rotateTiles();
- break;
- default:
- }
- };
+ canvas.onmousedown = (e: MouseEvent) => {
+ if (ImGui.GetIO().WantCaptureMouse) return;
+ demo.mouseButton('down');
+ };
+ canvas.onmouseup = (e: MouseEvent) => {
+ if (ImGui.GetIO().WantCaptureMouse) return;
+ demo.mouseButton('up');
+ };
+ canvas.onmousemove = (e: MouseEvent) => {
+ if (ImGui.GetIO().WantCaptureMouse) return;
+ // account for gl-origin vs. screen origin:
+ demo.mouseMove([-e.movementX, -e.movementY]);
+ };
+ canvas.onwheel = (e: WheelEvent) => {
+ if (e.shiftKey) {
+ demo.changeGamut(e.deltaY > 0 ? 1.1 : 0.9);
+ } else if (e.altKey) {
+ demo.changeSlice(e.deltaY > 0 ? 0.01 : -0.01);
+ } else {
+ demo.zoom(e.deltaY > 0 ? 1.1 : 0.9);
+ }
+ };
+ canvas.onkeydown = (e: KeyboardEvent) => {
+ switch (e.key) {
+ case 'a':
+ demo.nextAxis();
+ break;
+ case 'r':
+ demo.rotateTiles();
+ break;
+ default:
+ }
+ };
}
function setupGui(canvas: HTMLCanvasElement | WebGL2RenderingContext | WebGLRenderingContext) {
- ImGui.default().then(() => {
- ImGui.CHECKVERSION();
- ImGui.CreateContext();
- const io: ImGui.IO = ImGui.GetIO();
- ImGui.StyleColorsDark();
- io.Fonts.AddFontDefault();
- ImGui_Impl.Init(canvas);
- ImGui_Impl.ClearBuffer(new ImVec4(0.2, 0.2, 0.2, 1));
- });
+ ImGui.default().then(() => {
+ ImGui.CHECKVERSION();
+ ImGui.CreateContext();
+ const io: ImGui.IO = ImGui.GetIO();
+ ImGui.StyleColorsDark();
+ io.Fonts.AddFontDefault();
+ ImGui_Impl.Init(canvas);
+ ImGui_Impl.ClearBuffer(new ImVec4(0.2, 0.2, 0.2, 1));
+ });
}
async function demotime() {
- const ui = document.getElementById("uiCanvas") as HTMLCanvasElement;
- const yay = document.getElementById("glCanvas") as HTMLCanvasElement;
- yay.width = 2000;
- yay.height = 2000;
+ const ui = document.getElementById('uiCanvas') as HTMLCanvasElement;
+ const yay = document.getElementById('glCanvas') as HTMLCanvasElement;
+ yay.width = 2000;
+ yay.height = 2000;
- const gl = ui.getContext("webgl2", {
- alpha: true,
- preserveDrawingBuffer: true,
- antialias: true,
- premultipliedAlpha: true,
- }) as WebGL2RenderingContext;
+ const gl = ui.getContext('webgl2', {
+ alpha: true,
+ preserveDrawingBuffer: true,
+ antialias: true,
+ premultipliedAlpha: true,
+ }) as WebGL2RenderingContext;
- const regl = REGL({
- canvas: yay,
- attributes: {
- alpha: true,
- preserveDrawingBuffer: true,
- antialias: true,
- premultipliedAlpha: true,
- },
- extensions: ["ANGLE_instanced_arrays", "OES_texture_float", "WEBGL_color_buffer_float"],
- });
- ui.height = 2000;
- ui.width = 2000;
- const canvas: HTMLCanvasElement = regl._gl.canvas as HTMLCanvasElement;
- canvas.tabIndex = 3;
- setupGui(gl);
- const voxelSliceCache: AsyncDataCache = new AsyncDataCache((d: REGL.Texture2D) => {
- d.destroy()
- }, (_d) => 1, 200);
- const zarr = await load(file);
- explain(zarr);
+ const regl = REGL({
+ canvas: yay,
+ attributes: {
+ alpha: true,
+ preserveDrawingBuffer: true,
+ antialias: true,
+ premultipliedAlpha: true,
+ },
+ extensions: ['ANGLE_instanced_arrays', 'OES_texture_float', 'WEBGL_color_buffer_float'],
+ });
+ ui.height = 2000;
+ ui.width = 2000;
+ const canvas: HTMLCanvasElement = regl._gl.canvas as HTMLCanvasElement;
+ canvas.tabIndex = 3;
+ setupGui(gl);
+ const voxelSliceCache: AsyncDataCache = new AsyncDataCache<
+ string,
+ string,
+ REGL.Texture2D
+ >(
+ (d: REGL.Texture2D) => {
+ d.destroy();
+ },
+ (_d) => 1,
+ 200
+ );
+ const zarr = await load(file);
+ explain(zarr);
- const theDemo = new TissuecyteDemo(canvas, zarr, regl, voxelSliceCache, []);
+ const theDemo = new TissuecyteDemo(canvas, zarr, regl, voxelSliceCache, []);
- setupEventHandlers(canvas, theDemo);
- theDemo.rerender();
+ setupEventHandlers(canvas, theDemo);
+ theDemo.rerender();
}
// since I am just included in a script tag in a raw html document, this is how we start:
diff --git a/apps/omezarr-viewer/src/versa-renderer.ts b/apps/omezarr-viewer/src/versa-renderer.ts
index 6ce6605..0cb1f43 100644
--- a/apps/omezarr-viewer/src/versa-renderer.ts
+++ b/apps/omezarr-viewer/src/versa-renderer.ts
@@ -1,303 +1,307 @@
-import REGL, { type Framebuffer2D } from "regl";
-import { type ZarrDataset, type ZarrRequest, getSlice, pickBestScale, sizeInUnits, planeSizeInVoxels, indexOfDimension } from "Common/loaders/ome-zarr/zarr-data";
-import { Box2D, type Interval, Vec2, type box2D, type vec2, type vec4 } from "@alleninstitute/vis-geometry";
-import { omit, slice } from "lodash";
-import type { Camera } from "./camera";
-import type { NestedArray, TypedArray } from "zarr";
-import { getSlicePool } from "Common/loaders/ome-zarr/sliceWorkerPool";
-
-type Props = {
- target: Framebuffer2D | null;
- tile: vec4;
- view: vec4;
- rotation: number;
- Rgamut: vec2;
- Ggamut: vec2;
- Bgamut: vec2;
- viewport: REGL.BoundingBox;
- R: REGL.Texture2D;
- G: REGL.Texture2D;
- B: REGL.Texture2D;
-};
-function isTexture(obj: object | undefined): obj is Bfr {
- return (obj !== undefined && 'type' in obj && obj.type === 'texture2D')
-}
-export function buildVersaRenderer(regl: REGL.Regl) {
- const cmd = regl<
- {
- view: vec4;
- tile: vec4;
- rot: number;
- R: REGL.Texture2D;
- G: REGL.Texture2D;
- B: REGL.Texture2D;
- Rgamut: vec2;
- Ggamut: vec2;
- Bgamut: vec2;
- },
- { pos: REGL.BufferData },
- Props
- >({
- vert: ` precision highp float;
- attribute vec2 pos;
-
- uniform vec4 view;
- uniform vec4 tile;
- varying vec2 texCoord;
- uniform float rot;
-
- vec2 rotateObj(vec2 obj, float radians){
- return obj;
- }
- vec2 rotateTextureCoordinates(vec2 tx, float radians){
- vec2 xy = tx-vec2(0.5,0.5);
- mat2 R = mat2(
- vec2(cos(radians),-sin(radians)),
- vec2(-sin(radians),cos(radians))
- );
- return ((R*xy)+vec2(0.5,0.5));
- }
- void main(){
- vec2 tileSize = tile.zw-tile.xy;
- texCoord = rotateTextureCoordinates(pos,rot);
- vec2 obj = rotateObj((pos.xy*tileSize+tile.xy),rot);
-
- vec2 p = (obj-view.xy)/(view.zw-view.xy);
- // now, to clip space
- p = (p*2.0)-1.0;
- gl_Position = vec4(p.x,p.y,0.0,1.0);
- }`,
- frag: `
- precision highp float;
- uniform sampler2D R;
- uniform sampler2D G;
- uniform sampler2D B; // for reasons which are pretty annoying
- // its more direct to do 3 separate channels...
- uniform vec2 Rgamut;
- uniform vec2 Ggamut;
- uniform vec2 Bgamut;
-
- varying vec2 texCoord;
- void main(){
- vec3 mins = vec3(Rgamut.x,Ggamut.x,Bgamut.x);
- vec3 maxs = vec3(Rgamut.y,Ggamut.y,Bgamut.y);
- vec3 span = maxs-mins;
- vec3 color = (vec3(
- texture2D(R, texCoord).r,
- texture2D(G, texCoord).r,
- texture2D(B, texCoord).r
- )-mins) /span;
-
- gl_FragColor = vec4(color, 1.0);
- }`,
- framebuffer: regl.prop("target"),
- attributes: {
- pos: [0, 0, 1, 0, 1, 1, 0, 1],
- },
- uniforms: {
- rot: regl.prop("rotation"),
- tile: regl.prop("tile"),
- view: regl.prop("view"),
- R: regl.prop("R"),
- G: regl.prop("G"),
- B: regl.prop("B"),
- Rgamut: regl.prop("Rgamut"),
- Ggamut: regl.prop("Ggamut"),
- Bgamut: regl.prop("Bgamut"),
- },
- depth: {
- enable: false,
- },
- count: 4,
- // viewport: regl.prop("viewport"),
- primitive: "triangle fan",
- // ... more!
- });
-
- return (item: VoxelTile, settings: VoxelSliceRenderSettings, channels: Record) => {
- const { view, viewport, gamut, target, rotation } = settings;
- const { realBounds } = item;
- const { R, G, B } = channels;
-
- if (!isTexture(R) || !isTexture(G) || !isTexture(B)) {
- console.log("missing data: ", R, G, B);
- return;
- }
-
- cmd({
- target,
- rotation,
- view: [...view.minCorner, ...view.maxCorner],
- tile: [...realBounds.minCorner, ...realBounds.maxCorner],
- R: R.data,
- G: G.data,
- B: B.data,
- Rgamut: [gamut.R.gamut.min, gamut.R.gamut.max],
- Ggamut: [gamut.G.gamut.min, gamut.G.gamut.max],
- Bgamut: [gamut.B.gamut.min, gamut.B.gamut.max],
- });
- };
-}
-type Bfr = { type: 'texture2D', data: REGL.Texture2D };
-
-type Tile = { bounds: box2D };
-export type VoxelSliceRenderSettings = {
- regl: REGL.Regl;
- dataset: ZarrDataset;
- view: box2D;
- rotation: number;
- gamut: Record<"R" | "G" | "B", { gamut: Interval; index: number }>;
- viewport: REGL.BoundingBox;
- target: REGL.Framebuffer2D | null;
-};
-export type AxisAlignedPlane = "xy" | "yz" | "xz";
-export type VoxelTile = {
- plane: AxisAlignedPlane;
- realBounds: box2D;
- bounds: box2D; // in voxels, in the plane
- planeIndex: number;
- layerIndex: number;
- // time and channel are always = 0, for now
-};
-
-function toZarrRequest(tile: VoxelTile, channel: number): ZarrRequest {
- const { plane, planeIndex, bounds } = tile;
- const { minCorner: min, maxCorner: max } = bounds;
- const u = { min: min[0], max: max[0] };
- const v = { min: min[1], max: max[1] };
- switch (plane) {
- case "xy":
- return {
- x: u,
- y: v,
- t: 0,
- c: channel,
- z: planeIndex,
- };
- case "xz":
- return {
- x: u,
- z: v,
- t: 0,
- c: channel,
- y: planeIndex,
- };
- case "yz":
- return {
- y: u,
- z: v,
- t: 0,
- c: channel,
- x: planeIndex,
- };
- }
-}
-export function cacheKeyFactory(col: string, item: VoxelTile, settings: VoxelSliceRenderSettings) {
- return `${settings.dataset.url}_${JSON.stringify(omit(item, "desiredResolution"))}_ch=${settings.gamut[col as "R" | "G" | "B"].index
- }`;
-}
-
-function reqSlice(dataset: ZarrDataset, req: ZarrRequest, layerIndex: number) {
- return getSlicePool().requestSlice(dataset, req, layerIndex)
-}
-const LUMINANCE = "luminance";
-export function requestsForTile(tile: VoxelTile, settings: VoxelSliceRenderSettings, signal?: AbortSignal) {
- const { dataset, regl } = settings;
- const handleResponse = (vxl: Awaited>) => {
- const { shape, data } = vxl;
- const r = regl.texture({
- data,
- width: shape[1],
- height: shape[0], // TODO this swap is sus
- format: LUMINANCE,
- });
- return r;
- };
- // lets hope the browser caches our 3x repeat calls to teh same data...
- return {
- R: async () => {
- const vxl = await reqSlice(dataset, toZarrRequest(tile, settings.gamut.R.index), tile.layerIndex);
- return { type: 'texture2D', data: handleResponse(vxl) }
- },
- G: async () => {
- const vxl = await reqSlice(dataset, toZarrRequest(tile, settings.gamut.G.index), tile.layerIndex);
- return { type: 'texture2D', data: handleResponse(vxl) }
- },
- B: async () => {
- const vxl = await reqSlice(dataset, toZarrRequest(tile, settings.gamut.B.index), tile.layerIndex);
- return { type: 'texture2D', data: handleResponse(vxl) }
- },
- };
-}
-
-function getAllTiles(idealTilePx: vec2, layerSize: vec2) {
- // return the set of all our "tiles" of this layer, given the tilePx size
- const tiles: box2D[] = [];
- for (let x = 0; x < layerSize[0]; x += idealTilePx[0]) {
- for (let y = 0; y < layerSize[1]; y += idealTilePx[1]) {
- const xy: vec2 = [x, y];
- tiles.push(Box2D.create(xy, Vec2.min(Vec2.add(xy, idealTilePx), layerSize)));
- }
- }
- return tiles;
-}
-const uvTable = {
- xy: { u: "x", v: "y" },
- xz: { u: "x", v: "z" },
- yz: { u: "y", v: "z" },
-} as const;
-const sliceDimension = {
- xy: "z",
- xz: "y",
- yz: "x",
-} as const;
-
-export function getVisibleTiles(
- camera: Camera,
- plane: AxisAlignedPlane,
- planeIndex: number,
- dataset: ZarrDataset,
- offset?: vec2
-): { layer: number; view: box2D; tiles: VoxelTile[] } {
- // const { axes, datasets } = dataset.multiscales[0];
- // const zIndex = indexOfDimension(axes, sliceDimension[plane]);
- const sliceSize = sizeInUnits(
- uvTable[plane],
- dataset.multiscales[0].axes,
- dataset.multiscales[0].datasets[0]
- )!;
- const layer = pickBestScale(
- dataset,
- uvTable[plane],
- camera.view,
- camera.screen
- );
- // TODO: open the array, look at its chunks, use that size for the size of the tiles I request!
- const layerIndex = dataset.multiscales[0].datasets.indexOf(layer);
-
- const size = planeSizeInVoxels(uvTable[plane], dataset.multiscales[0].axes, layer);
- const realSize = sizeInUnits(uvTable[plane], dataset.multiscales[0].axes, layer);
- if (!size || !realSize) return { layer: layerIndex, view: Box2D.create([0, 0], [1, 1]), tiles: [] };
- const scale = Vec2.div(realSize, size);
- // to go from a voxel-box to a real-box (easier than you think, as both have an origin at 0,0, because we only support scale...)
- const vxlToReal = (vxl: box2D) => Box2D.translate(Box2D.scale(vxl, scale), offset ?? [0, 0]);
- // const realToVxl = (real: box2D) => Box2D.scale(real, Vec2.div(size, realSize));
-
- // find the tiles, in voxels, to request...
- const allTiles = getAllTiles([256, 256], size);
- const inView = allTiles.filter((tile) => !!Box2D.intersection(camera.view, vxlToReal(tile)));
- // camera.view is in a made up dataspace, where 1=height of the current dataset
- // thus, we have to convert it into a voxel-space camera for intersections
- // const voxelView = realToVxl(camera.view);
- return {
- layer: layerIndex,
- view: camera.view,
- tiles: inView.map((uv) => ({
- plane,
- realBounds: vxlToReal(uv),
- bounds: uv,
- planeIndex,
- layerIndex,
- })),
- };
-}
+import REGL, { type Framebuffer2D } from 'regl';
+import {
+ type ZarrDataset,
+ type ZarrRequest,
+ getSlice,
+ pickBestScale,
+ sizeInUnits,
+ planeSizeInVoxels,
+ indexOfDimension,
+} from 'Common/loaders/ome-zarr/zarr-data';
+import { Box2D, type Interval, Vec2, type box2D, type vec2, type vec4 } from '@alleninstitute/vis-geometry';
+import { omit, slice } from 'lodash';
+import type { Camera } from './camera';
+import type { NestedArray, TypedArray } from 'zarr';
+import { getSlicePool } from 'Common/loaders/ome-zarr/sliceWorkerPool';
+
+type Props = {
+ target: Framebuffer2D | null;
+ tile: vec4;
+ view: vec4;
+ rotation: number;
+ Rgamut: vec2;
+ Ggamut: vec2;
+ Bgamut: vec2;
+ viewport: REGL.BoundingBox;
+ R: REGL.Texture2D;
+ G: REGL.Texture2D;
+ B: REGL.Texture2D;
+};
+function isTexture(obj: object | undefined): obj is Bfr {
+ return obj !== undefined && 'type' in obj && obj.type === 'texture2D';
+}
+export function buildVersaRenderer(regl: REGL.Regl) {
+ const cmd = regl<
+ {
+ view: vec4;
+ tile: vec4;
+ rot: number;
+ R: REGL.Texture2D;
+ G: REGL.Texture2D;
+ B: REGL.Texture2D;
+ Rgamut: vec2;
+ Ggamut: vec2;
+ Bgamut: vec2;
+ },
+ { pos: REGL.BufferData },
+ Props
+ >({
+ vert: ` precision highp float;
+ attribute vec2 pos;
+
+ uniform vec4 view;
+ uniform vec4 tile;
+ varying vec2 texCoord;
+ uniform float rot;
+
+ vec2 rotateObj(vec2 obj, float radians){
+ return obj;
+ }
+ vec2 rotateTextureCoordinates(vec2 tx, float radians){
+ vec2 xy = tx-vec2(0.5,0.5);
+ mat2 R = mat2(
+ vec2(cos(radians),-sin(radians)),
+ vec2(-sin(radians),cos(radians))
+ );
+ return ((R*xy)+vec2(0.5,0.5));
+ }
+ void main(){
+ vec2 tileSize = tile.zw-tile.xy;
+ texCoord = rotateTextureCoordinates(pos,rot);
+ vec2 obj = rotateObj((pos.xy*tileSize+tile.xy),rot);
+
+ vec2 p = (obj-view.xy)/(view.zw-view.xy);
+ // now, to clip space
+ p = (p*2.0)-1.0;
+ gl_Position = vec4(p.x,p.y,0.0,1.0);
+ }`,
+ frag: `
+ precision highp float;
+ uniform sampler2D R;
+ uniform sampler2D G;
+ uniform sampler2D B; // for reasons which are pretty annoying
+ // its more direct to do 3 separate channels...
+ uniform vec2 Rgamut;
+ uniform vec2 Ggamut;
+ uniform vec2 Bgamut;
+
+ varying vec2 texCoord;
+ void main(){
+ vec3 mins = vec3(Rgamut.x,Ggamut.x,Bgamut.x);
+ vec3 maxs = vec3(Rgamut.y,Ggamut.y,Bgamut.y);
+ vec3 span = maxs-mins;
+ vec3 color = (vec3(
+ texture2D(R, texCoord).r,
+ texture2D(G, texCoord).r,
+ texture2D(B, texCoord).r
+ )-mins) /span;
+
+ gl_FragColor = vec4(color, 1.0);
+ }`,
+ framebuffer: regl.prop('target'),
+ attributes: {
+ pos: [0, 0, 1, 0, 1, 1, 0, 1],
+ },
+ uniforms: {
+ rot: regl.prop('rotation'),
+ tile: regl.prop('tile'),
+ view: regl.prop('view'),
+ R: regl.prop('R'),
+ G: regl.prop('G'),
+ B: regl.prop('B'),
+ Rgamut: regl.prop