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Commits on Jul 1, 2022

• Examples README

  

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• steinbock_notebook v1.0.0

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• jupytext

  

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Commits on Jul 4, 2022

• add script to download examples and panel

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• updated path to proper panel

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• updated panel and image conversion

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• add helper functions

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Commits on Jul 6, 2022

• Fix duplicated names in panel.csv

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• small changes for consistency with steinbock docker

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• put normalization functions in helpers

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• make all output file names identical

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Commits on Jul 7, 2022

• make sure deepcell channels are not 0

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• run segmentation with deepcell, not steinbock

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Commits on Jul 15, 2022

• new example script for IF data

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• generate stacks from single tiffs

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Commits on Aug 18, 2022

• read imgs/masks with tifffile for IF measurements

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Commits on Aug 24, 2022

• add jupytext

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• download example data from main notebook

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• create panel from mcd

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• read panel with

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• use steinbock for deepcell segmentation

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• cell segmentation check: show image+mask overlay

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Commits on Aug 25, 2022

• split up the notebooks

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Commits on Aug 27, 2022

• closes #139

  

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• closes #140

  

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• closes #141

  

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• typing

  

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• rename function

  

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• typing

  

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Commits on Aug 29, 2022

• use steinbock function for zip extraction

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• update installation instructions

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• use imc.create_image_info() to extract image metadata

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• create seg stacks with deepcell.create_segmentation_stack()

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• update .py files jupytext + delete helpers.py

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Commits on Sep 13, 2022

• Fix histoCAT mask export (closes #136)

  

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• docs (closes #121)

  

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• closes #139

  

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• closes #140

  

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• closes #141

  

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• typing

  

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Commits on Sep 14, 2022

• support 2-6 channel TIFFs (closes #109)

  

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• process data from zips individually (closes #117)

  

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• docs

  

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• fix relabeling during stitching (closes #146)

  

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• explain Docker run options (closes #104)

  

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• dependency upgrades

  

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Commits on Sep 15, 2022

• Fix CellProfiler version

  

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• fix default skimage regionprops

  

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• anndata export panel/image metadata (closes #66)

  

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• v0.15.0

  

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• Merge pull request #147 from BodenmillerGroup/develop

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• Examples README

  

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• steinbock_notebook v1.0.0

  

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• jupytext

  

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• extract ome.tiff and metadata

  

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• add script to download examples and panel

  

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• updated path to proper panel

  

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• updated panel and image conversion

  

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• add helper functions

  

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• Fix duplicated names in panel.csv

  

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• small changes for consistency with steinbock docker

  

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• put normalization functions in helpers

  

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• make all output file names identical

  

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• make sure deepcell channels are not 0

  

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• run segmentation with deepcell, not steinbock

  

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• new example script for IF data

  

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• generate stacks from single tiffs

  

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• read imgs/masks with tifffile for IF measurements

  

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• add jupytext

  

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• download example data from main notebook

  

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• create panel from mcd

  

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• read panel with

  

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• use steinbock for deepcell segmentation

  

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• cell segmentation check: show image+mask overlay

  

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• split up the notebooks

  

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• Delete panel.csv

  

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• use steinbock function for zip extraction

  

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• update installation instructions

  

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• use imc.create_image_info() to extract image metadata

  

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• create seg stacks with deepcell.create_segmentation_stack()

  

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• update .py files jupytext + delete helpers.py

  

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• Merge branch 'examples' of github.com:BodenmillerGroup/steinbock into examples

  

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Commits on Oct 31, 2022

• changes for steinbock v0.15

  

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Commits on Dec 12, 2022

• update installation instructions

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• update insallation instructions - pyfiles

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