Merge branch '1-developing-practical-1' into main

elixir-europe-training · Nov 13, 2024 · 73fd93d · 73fd93d
2 parents 58cbda5 + 09faca6
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diff --git a/day_1/practical_1/3D Nucleus Segmentation with Cellpose.ipynb b/day_1/practical_1/3D Nucleus Segmentation with Cellpose.ipynb
diff --git a/day_1/practical_1/cellpose_env.yml b/day_1/practical_1/cellpose_env.yml
@@ -0,0 +1,13 @@
+name: cellpose_env
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - python=3.9
+  - pip
+  - tifffile
+  - matplotlib
+  - numpy
+  - scikit-image
+  - pip:
+      - cellpose
diff --git a/day_1/practical_1/custom/__pycache__/tenx_method_nb_helper_functions.cpython-39.pyc b/day_1/practical_1/custom/__pycache__/tenx_method_nb_helper_functions.cpython-39.pyc
diff --git a/day_1/practical_1/custom/tenx_method_nb_helper_functions.py b/day_1/practical_1/custom/tenx_method_nb_helper_functions.py
diff --git a/day_1/practical_1/extract_tiff.py b/day_1/practical_1/extract_tiff.py
@@ -0,0 +1,20 @@
+#!/usr/bin/env python
+
+import tifffile
+
+# Variable 'LEVEL' determines the level to extract. It ranges from 0 (highest
+# resolution) to 6 (lowest resolution) for morphology.ome.tif
+LEVEL = 2
+
+with tifffile.TiffFile('data/xenium_2.0.0_io/morphology.ome.tif') as tif:
+    image = tif.series[0].levels[LEVEL].asarray()
+
+tifffile.imwrite(
+    'level_'+str(LEVEL)+'_morphology.ome.tif',
+    image,
+    photometric='minisblack',
+    dtype='uint16',
+    tile=(1024, 1024),
+    compression='JPEG_2000_LOSSY',
+    metadata={'axes': 'ZYX'},
+)
diff --git a/day_1/practical_1/extract_tiff_metadata.py b/day_1/practical_1/extract_tiff_metadata.py
@@ -0,0 +1,8 @@
+#!/usr/bin/env python
+
+import tifffile
+
+with tifffile.TiffFile('data/xenium_2.0.0_io/morphology.ome.tif') as tif:
+    for tag in tif.pages[0].tags.values():
+        if tag.name == "ImageDescription":
+            print(tag.name+":", tag.value)
diff --git a/day_1/practical_1/imaging_based_data_analysis_env.yml b/day_1/practical_1/imaging_based_data_analysis_env.yml
@@ -24,4 +24,5 @@ dependencies:
   - jupyterlab-system-monitor
   - jupyterlab-dash
   - pip
-  - spatialdata_plot
+  - spatialdata_plot
+  - diptest
diff --git a/day_1/practical_1/practical_1_2.ipynb b/day_1/practical_1/practical_1_2.ipynb