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base repository: MannLabs/scPortrait-notebooks
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base: 7d2335d37f26e4c0bef1da3fa7cc8cc00b622af6
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head repository: MannLabs/scPortrait-notebooks
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compare: bd8f8f041aa02bd4d18f1be4655f9e7cc4dfa307
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  • 1 commit
  • 3 files changed
  • 1 contributor

Commits on Dec 9, 2024

  1. Verified

    This commit was signed with the committer’s verified signature.
    jkoenig134 Julian König
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    bd8f8f0 View commit details
Showing with 996 additions and 0 deletions.
  1. +36 −0 development/config_example1.yml
  2. +515 −0 development/processing_notebook.ipynb
  3. +445 −0 development/processing_notebook_sharded.ipynb
36 changes: 36 additions & 0 deletions development/config_example1.yml
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---
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: "."
515 changes: 515 additions & 0 deletions development/processing_notebook.ipynb

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445 changes: 445 additions & 0 deletions development/processing_notebook_sharded.ipynb

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