MannLabs · Dec 9, 2024
Showing with 996 additions and 0 deletions.

+36 −0 development/config_example1.yml

+515 −0 development/processing_notebook.ipynb

+445 −0 development/processing_notebook_sharded.ipynb
diff --git a/development/config_example1.yml b/development/config_example1.yml
@@ -0,0 +1,36 @@
+---
+name: "WGA confluent segmentation"
+input_channels: 3
+output_channels: 5
+CytosolSegmentationCellpose:
+    chunk_size: 50 # chunk size for chunked HDF5 storage. is needed for correct caching and high performance reading. should be left at 50.
+    cache: "."
+    combine_cytosol_channels: [1, 2]
+    nucleus_segmentation:
+        model: "nuclei"
+    cytosol_segmentation:
+        model: "cyto2"
+    chunk_size: 50
+    match_masks: True
+    filtering_threshold_mask_matching: 0.95
+    filter_masks_size: False
+ShardedCytosolSegmentationCellpose:
+    shard_size: 12000000 # maxmimum number of pixel per tile
+    overlap_px: 100
+    nGPUs: 1
+    chunk_size: 50 # chunk size for chunked HDF5 storage. is needed for correct caching and high performance reading. should be left at 50.
+    threads: 1 # number of shards / tiles segmented at the same size. should be adapted to the maximum amount allowed by memory.
+    cache: "."
+    combine_cytosol_channels: [1, 2]
+    nucleus_segmentation:
+        model: "nuclei"
+    cytosol_segmentation:
+        model: "cyto2"
+    chunk_size: 50
+    match_masks: True
+    filtering_threshold_mask_matching: 0.95
+    filter_masks_size: False
+HDF5CellExtraction:
+    threads: 80 # threads used in multithreading
+    image_size: 128 # image size in pixel
+    cache: "."
diff --git a/development/processing_notebook.ipynb b/development/processing_notebook.ipynb
diff --git a/development/processing_notebook_sharded.ipynb b/development/processing_notebook_sharded.ipynb