create labels with an extra dimension for 1 channel and set colormaps…

… in sample data
MontpellierRessourcesImagerie · Nov 26, 2024 · 446345f · 446345f
1 parent 1113fb7
commit 446345f
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Showing 2 changed files with 20 additions and 10 deletions.
diff --git a/src/segment_embryo/_sample_data.py b/src/segment_embryo/_sample_data.py
@@ -20,26 +20,33 @@ def make_sample_data():
     # Check the documentation for more information about the
     # add_image_kwargs
     # https://napari.org/stable/api/napari.Viewer.html#napari.Viewer.add_image
-    scale = (1000, 76.0005, 76.0005	)
+    scale = (1, 1000, 76.0005, 76.0005)
+    units = ('pixel', 'nm', 'nm', 'nm')
     nucleiData = io.imread('https://dev.mri.cnrs.fr/attachments/download/3597/C1-240628_DAPI_MEMBRITE-546_EPHA-488_TBXT-594_OTX-647_SLOWFADE_2.tif')
-    nuclei = numpy.array(nucleiData)
+    nuclei = numpy.array([numpy.array(nucleiData)])
     spotsData = io.imread('https://dev.mri.cnrs.fr/attachments/download/3595/C4-240628_DAPI_MEMBRITE-546_EPHA-488_TBXT-594_OTX-647_SLOWFADE_2.tif')
-    spots = numpy.array(spotsData)
+    spots = numpy.array([numpy.array(spotsData)])
     membranesData = io.imread('https://dev.mri.cnrs.fr/attachments/download/3596/C5-240628_DAPI_MEMBRITE-546_EPHA-488_TBXT-594_OTX-647_SLOWFADE_2.tif')
-    membranes = numpy.array(membranesData)
+    membranes = numpy.array([numpy.array(membranesData)])
 
     return [(nuclei,
              {'scale': scale,
-              'units':  ('nm', 'nm', 'nm'),
+              'units':  units,
+              'colormap': 'bop blue',
+              'blending': "additive",
               'name': 'nuclei (segment-embryo example image)'}),
             (spots,
              {'scale': scale,
-              'units': ('nm', 'nm', 'nm'),
+              'units': units,
+              'colormap': 'red',
+              'blending': "additive",
               'name': 'spots (segment-embryo example image)'},
              ),
             (membranes,
              {'scale': scale,
-              'units': ('nm', 'nm', 'nm'),
+              'units': units,
+              'colormap': 'bop orange',
+              'blending': "additive",
               'name': 'membranes (segment-embryo example image)'},
              )
             ]
diff --git a/src/segment_embryo/_widget.py b/src/segment_embryo/_widget.py
@@ -1,5 +1,7 @@
 import time
 from typing import TYPE_CHECKING
+
+import numpy as np
 from PyQt5.QtWidgets import QGroupBox, QFormLayout, QVBoxLayout
 from qtpy.QtWidgets import QHBoxLayout, QPushButton, QWidget
 from segment_embryo.napari_util import NapariUtil
@@ -91,10 +93,11 @@ def updateLayerSelectionComboBoxes(self):
     def _new_segmentation(self, mask):
         membranesLayerName = self.membranesLayerCombo.currentText()
         name = "Labels of " + membranesLayerName
-        self.viewer.add_labels(mask, name=name)
-        self.viewer.layers[name].scale = self.viewer.layers[membranesLayerName].scale[-3: ]
+        maskImage = np.array([mask])
+        self.viewer.add_labels(maskImage, name=name)
+        self.viewer.layers[name].scale = self.viewer.layers[membranesLayerName].scale[-4: ]
         self.viewer.layers[name].translate = self.viewer.layers[membranesLayerName].translate[-3: ]
-        self.viewer.layers[name].units = self.viewer.layers[membranesLayerName].units[-3: ]
+        self.viewer.layers[name].units = self.viewer.layers[membranesLayerName].units[-4: ]
         self.progressThread.stop()