From c3c24c4c751f66e42df7b5146d994eb32003382b Mon Sep 17 00:00:00 2001 From: Anna Grim <108307071+anna-grim@users.noreply.github.com> Date: Wed, 8 Jan 2025 16:42:35 -0800 Subject: [PATCH] minor upds --- tutorials/1-soma_proposal_generation.ipynb | 14 ++++---- tutorials/exaspim_image_prefixes.json | 39 ++++++++++++++++++++++ 2 files changed, 46 insertions(+), 7 deletions(-) create mode 100644 tutorials/exaspim_image_prefixes.json diff --git a/tutorials/1-soma_proposal_generation.ipynb b/tutorials/1-soma_proposal_generation.ipynb index 6b2487c..20d6dab 100644 --- a/tutorials/1-soma_proposal_generation.ipynb +++ b/tutorials/1-soma_proposal_generation.ipynb @@ -29,9 +29,8 @@ " Soma Proposal Generation Algorithm\n", " 1. Generate Initial Proposals - detect_blobs()\n", " a. Smooth image with Gaussian filter to reduce false positives.\n", - " b. Laplacian of Gaussian (LoG) to enhance regions where the\n", - " intensity changes dramatically (i.e. higher gradient), then\n", - " apply a non-linear maximum filter.\n", + " b. Laplacian of Gaussian (LoG) to enhance regions where the gradient\n", + " changes rapidly, then apply a non-linear maximum filter.\n", " c. Generate initial set of proposals by detecting local maximas\n", " that lie outside of the image margins.\n", " d. Shift each proposal to the brightest voxel in its neighborhood.\n", @@ -201,7 +200,7 @@ "\n", "# Proposals: 1\n", "# Rejects: 0\n", - "Runtime: 0.2150118350982666\n" + "Runtime: 0.21765899658203125\n" ] }, { @@ -277,6 +276,7 @@ "proposals = spg.brightness_filtering(img_patch, proposals, 10)\n", "proposals, rejects = gaussian_fitness_filtering(img_patch, proposals)\n", "\n", + "# Report Results\n", "print(\"\\n# Proposals:\", len(proposals))\n", "print(\"# Rejects:\", len(rejects))\n", "print(\"Runtime:\", time() - t0)\n", @@ -445,7 +445,7 @@ "name": "stderr", "output_type": "stream", "text": [ - "100%|██████████| 100/100 [00:07<00:00, 3.70it/s]" + "100%|██████████| 100/100 [00:05<00:00, 15.45it/s]" ] }, { @@ -454,14 +454,14 @@ "text": [ "\n", "# Proposals Generated: 11\n", - "Runtime: 7.499921083450317\n" + "Runtime: 5.63988184928894\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "101it [00:19, 3.70it/s] " + "101it [00:19, 15.45it/s] " ] } ], diff --git a/tutorials/exaspim_image_prefixes.json b/tutorials/exaspim_image_prefixes.json new file mode 100644 index 0000000..eae7c80 --- /dev/null +++ b/tutorials/exaspim_image_prefixes.json @@ -0,0 +1,39 @@ +{ + "516429": "s3://aind-open-data/exaSPIM_516429_2023-08-23_14-58-20_fusion_2023-09-18/fused.zarr/", + "613814": "s3://aind-open-data/exaSPIM_613814_2023-04-15_13-02-26_fusion_2023-04-26_15-08-00/fused.zarr/", + "648434": "s3://aind-open-data/exaSPIM_648434_2023-08-29_15-00-36_fusion_2023-09-22/fused.zarr/", + "650010": "s3://aind-open-data/exaSPIM_650010_2023-04-04_17-42-51_fusion_2023-04-23_11-35-00/fused.zarr/", + "650011": "s3://aind-open-data/exaSPIM_650011_2023-04-08_08-21-34_fusion_2023-05-17_18-41-00/fused.zarr/", + "651324": "s3://aind-open-data/exaSPIM_651324_2023-03-06_15-13-25_fusion_2023-03-28_17-06-00/fused.zarr/", + "651895": "s3://aind-open-data/exaSPIM_651895_2023-09-08_10-16-01_fusion_2023-09-26/fused.zarr/", + "657676": "s3://aind-open-data/exaSPIM_657676_2023-10-27_12-31-24_fusion_2023-11-25_22-28-00/fused.zarr/", + "653158": "s3://aind-open-data/exaSPIM_653158_2023-06-01_20-41-38_fusion_2023-06-12_11-58-05/fused.zarr/", + "653159": "s3://aind-open-data/exaSPIM_653159_2024-02-05_15-38-38_fusion_2024-02-21_01-44-06/fused.zarr/", + "653980": "s3://aind-open-data/exaSPIM_653980_2023-08-10_20-08-29_fusion_2023-08-24/fused.zarr/", + "658735": "s3://aind-open-data/exaSPIM_658735_2023-08-15_16-13-50_fusion_2023-09-01/fused.zarr/", + "665081": "s3://aind-open-data/exaSPIM_665081_2023-09-18_15-20-19_fusion_2023-12-18_17-28-00/fused.zarr/", + "667996": "s3://aind-open-data/exaSPIM_667996_2024-03-05_17-26-26_fusion_2024-04-02_23-17-06/fused.zarr/", + "671477": "s3://aind-open-data/exaSPIM_671477_2024-01-08_17-03-04_fusion_2024-01-23_20-56-20/fused.zarr/", + "674185": "s3://aind-open-data/exaSPIM_674185_2023-10-02_14-06-36_flatfield-correction_2023-11-17_00-33-17_fusion_2023-11-23_12-56-00/fused.zarr/", + 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