arbitrary number of imaging layers in zarr (#76)

* arbitrary number of imaging layers in zarr

* descriptive error message when layer names list does not match number of channels in zarr

Author: TeunHuijben

.gitignore

@@ -166,6 +166,8 @@ cython_debug/
 
 # vscode files
 .history
+.vscode/
+CLAUDE.md
 
 # Ignore examples files
 examples/*/*

pixi.lock

@@ -39,10 +39,10 @@ extra-dependencies = [
   "mypy>=1.0.0",
 ]
 [tool.hatch.envs.types.scripts]
-check = "mypy --install-types --non-interactive {args:trackedit tests}"
+check = "mypy --install-types --non-interactive {args:trackedit trackedit/_tests}"
 
 [tool.coverage.run]
-source_pkgs = ["trackedit", "tests"]
+source_pkgs = ["trackedit", "trackedit/_tests"]
 branch = true
 parallel = true
 omit = [
@@ -51,7 +51,7 @@ omit = [
 
 [tool.coverage.paths]
 trackedit = ["trackedit", "*/trackedit/trackedit"]
-tests = ["tests", "*/trackedit/tests"]
+tests = ["trackedit/_tests", "*/trackedit/trackedit/_tests"]
 
 [tool.coverage.report]
 exclude_lines = [
@@ -90,6 +90,7 @@ pyqt = ">=5.15.9,<6"
 numpy = "<2.2"
 pre-commit = ">=4.1.0,<5"
 dask = ">=2025.2.0,<2026"
+pytest = ">=8.4.2,<9"
 
 [tool.pixi.feature.test.dependencies]
 pytest = "*"

pyproject.toml

@@ -27,7 +27,7 @@
 
 # OPTIONAL: imaging data
 imaging_zarr_file = (
-    "/hpc/projects/intracellular_dashboard/organelle_dynamics/rerun/"
+    "/hpc/projects/intracellular_dashboard/organelle_dynamics/"
     "2025_07_24_A549_SEC61_TOMM20_G3BP1_ZIKV/2-assemble/"
     "2025_07_24_A549_SEC61_TOMM20_G3BP1_ZIKV.zarr/A/1/000000/"
 )

scripts/script_cropped_fov.py

@@ -58,6 +58,7 @@ def __init__(
         image_translate: tuple = None,
         coordinate_filters: list = None,
         default_start_annotation: int = None,  # Make it optional
+        imaging_layer_names: list = None,
     ):
 
         # inputs
@@ -75,8 +76,11 @@ def __init__(
         self.imaging_channel = imaging_channel
         self.image_z_slice = image_z_slice
         self.image_translate = image_translate
-        self.imaging_flag = True if self.imaging_zarr_file is not None else False
+        self.imaging_flag = (
+            True if self.imaging_zarr_file and self.imaging_zarr_file != "" else False
+        )
         self.coordinate_filters = coordinate_filters
+        self.imaging_layer_names = imaging_layer_names
 
         # Filenames / directories
         self.extension_string = ""
@@ -175,6 +179,7 @@ def __init__(
                 channel=self.imaging_channel,
                 time_window=self.time_window,
                 image_z_slice=self.image_z_slice,
+                imaging_layer_names=self.imaging_layer_names,
             )
         self.df_full = self.db_to_df(entire_database=True)
 

trackedit/DatabaseHandler.py

@@ -72,27 +72,28 @@ def __init__(
             color_dict=self.databasehandler.color_mapping
         )
 
-        # Add Imaging layer to viewer
+        # Add Imaging layers to viewer
         if self.databasehandler.imaging_flag:
-            layer_nuc = self.viewer.add_image(
-                self.databasehandler.imagingArray.nuclear,
-                name="im_nuclear",
-                colormap="green",
-                scale=self.databasehandler.scale,
-                visible=False,
-                translate=self.databasehandler.image_translate,
-            )
-            layer_nuc.reset_contrast_limits()
-            layer_mem = self.viewer.add_image(
-                self.databasehandler.imagingArray.membrane,
-                name="im_membrane",
-                colormap="red",
-                opacity=0.5,
-                scale=self.databasehandler.scale,
-                visible=False,
-                translate=self.databasehandler.image_translate,
-            )
-            layer_mem.reset_contrast_limits()
+            # Define colormap sequence
+            colormaps = ["green", "red", "blue", "magenta", "cyan", "yellow"]
+
+            for i, layer_name in enumerate(
+                self.databasehandler.imagingArray.layer_names
+            ):
+                channel_data = self.databasehandler.imagingArray.get_channel_data(i)
+                colormap = colormaps[i % len(colormaps)]
+                opacity = 1.0 if i == 0 else 0.5  # First layer full opacity, others 0.5
+
+                layer = self.viewer.add_image(
+                    channel_data,
+                    name=f"im_{layer_name}",
+                    colormap=colormap,
+                    opacity=opacity,
+                    scale=self.databasehandler.scale,
+                    visible=False,
+                    translate=self.databasehandler.image_translate,
+                )
+                layer.reset_contrast_limits()
 
         tabwidget_bottom = QTabWidget()
         tabwidget_bottom.addTab(self.TreeWidget, "TreeWidget")
@@ -188,12 +189,11 @@ def update_chunk_from_button(self, direction: str):
         self.databasehandler.set_time_chunk(new_chunk)
         self.update_hierarchy_layer()
         if self.databasehandler.imaging_flag:
-            self.viewer.layers[
-                "im_nuclear"
-            ].data = self.databasehandler.imagingArray.nuclear
-            self.viewer.layers[
-                "im_membrane"
-            ].data = self.databasehandler.imagingArray.membrane
+            for i, layer_name in enumerate(
+                self.databasehandler.imagingArray.layer_names
+            ):
+                channel_data = self.databasehandler.imagingArray.get_channel_data(i)
+                self.viewer.layers[f"im_{layer_name}"].data = channel_data
 
         self.add_tracks()
 
@@ -244,12 +244,11 @@ def update_chunk_from_frame(self, frame: int):
         self.databasehandler.set_time_chunk(new_chunk)
         self.update_hierarchy_layer()
         if self.databasehandler.imaging_flag:
-            self.viewer.layers[
-                "im_nuclear"
-            ].data = self.databasehandler.imagingArray.nuclear
-            self.viewer.layers[
-                "im_membrane"
-            ].data = self.databasehandler.imagingArray.membrane
+            for i, layer_name in enumerate(
+                self.databasehandler.imagingArray.layer_names
+            ):
+                channel_data = self.databasehandler.imagingArray.get_channel_data(i)
+                self.viewer.layers[f"im_{layer_name}"].data = channel_data
 
         # Update tracks if chunks are different OR if this was triggered by a Tmax change
         # TODO: not sure this is the best way to do this