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angelolab
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ark-analysis
Integrated pipeline for multiplexed image analysis
https://ark-analysis.readthedocs.io/en/latest/
MIT License
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25
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"Commercial use" license inquiry
#1044
VictorDidier
closed
1 year ago
2
Fix color_map setting in visualization notebook
#1043
camisowers
closed
1 year ago
0
Update README with Pixie reference
#1042
cliu72
closed
1 year ago
0
Update reference to pixie paper
#1041
ngreenwald
closed
1 year ago
0
Changing cmap colors in the visualization notebook
#1040
Zach-Sten
closed
1 year ago
0
Updating deepcell_visualization files after filtering for too small/too big cells from the cell table
#1039
TerGla
opened
1 year ago
4
Adding cropping utility notebook for Pixie
#1038
cliu72
opened
1 year ago
2
Generic Segmentation Masks Notebook and Continuous Cmaps
#1037
srivarra
closed
11 months ago
4
Allow for fewer than specified SOM clusters to be contained in Pixie average file
#1036
alex-l-kong
closed
1 year ago
1
Local Deepcell or Cellpose server for larger tile segmentation
#1035
jamesMo84
opened
1 year ago
2
Bump to v0.6.5
#1033
alex-l-kong
closed
1 year ago
2
Update progress bars
#1031
camisowers
closed
1 year ago
1
Mask Generation Refactoring
#1030
srivarra
closed
11 months ago
2
Make file path selection more interactive
#1029
alex-l-kong
opened
1 year ago
0
Update progress bar for helpful debugging
#1028
camisowers
closed
1 year ago
0
Optional normalization for generic_cell_clustering.ipynb
#1027
camisowers
closed
1 year ago
1
Dependency conflicts between pyproject.toml and environment.yml
#1026
camisowers
closed
1 year ago
3
Maximize Available GitHub Storage Space
#1025
srivarra
closed
1 year ago
1
Ubuntu Linux GHA Runner caps the provided Storage
#1024
srivarra
closed
1 year ago
0
Deepcell upload loop cleaning
#1023
camisowers
closed
1 year ago
1
Add progress bars in Cell Neighbors Analysis notebook
#1022
camisowers
closed
1 year ago
0
Allow FOVs to contain various maximum clusters
#1021
srivarra
closed
1 year ago
1
Pixie percentile saving
#1020
camisowers
closed
1 year ago
1
Progress bars for spatial analysis
#1019
camisowers
closed
1 year ago
0
Drop 3rd dimension in segmentation masks
#1018
camisowers
closed
1 year ago
1
In pixel clustering, if restarting `create_pixel_matrix`, not all FOVs are used to find the 99.9th percentile values
#1016
cliu72
closed
1 year ago
0
Mixing score default thresholds
#1015
camisowers
closed
1 year ago
1
Include all fiber properties in stats generation
#1014
camisowers
closed
1 year ago
0
Missing docker import: alpineer
#1013
dtebaykin
closed
1 year ago
1
Next Release v0.6.4
#1012
srivarra
closed
1 year ago
1
Fix error from zero fibers in an image
#1011
camisowers
closed
1 year ago
0
Cell mask generation assumes all FOVs have the same maximum cluster number
#1010
cliu72
closed
1 year ago
1
Issue with segmentation mask stitching
#1009
camisowers
closed
1 year ago
3
Fix segmentation rescale_factor
#1008
camisowers
closed
1 year ago
0
Save Colored Pixie Masks
#1007
srivarra
closed
1 year ago
1
Added Conda environment file
#1006
srivarra
closed
1 year ago
0
:arrow_up: Bump pypa/cibuildwheel from 2.11.4 to 2.13.0
#1005
dependabot[bot]
closed
1 year ago
1
Issue setting up the repo on Windows
#1004
jlqm2
closed
1 year ago
3
Bump requests from 2.28.0 to 2.31.0 in /docs
#1003
dependabot[bot]
opened
1 year ago
0
rescale_factor not affecting segmentation
#1001
ngreenwald
closed
1 year ago
0
Make 99.9 normalization optional on function cell_som_clustering.train_cell_som
#1000
JLrumberger
closed
1 year ago
1
Add fallback protection to Pixie cell clustering
#999
alex-l-kong
closed
1 year ago
1
Pixel Clustering - Run without segmentaiton files
#998
srivarra
closed
1 year ago
1
Save the colored pixel/cell phenotype maps at the end of the Pixie notebooks
#997
cliu72
closed
1 year ago
0
Make it easier if `segmentation_dir=None` in pixel clustering notebook
#996
cliu72
closed
1 year ago
0
Add Pixie notebook tests that account for non-linear workflows
#995
alex-l-kong
opened
1 year ago
0
Mantis Directory with no segmentation files
#994
srivarra
closed
1 year ago
0
Prevent duplicate renamed metaclusters in Pixie remapping
#993
alex-l-kong
closed
1 year ago
1
Save `cluster_counts_size_norm` as it is being updated
#992
HPiyadasa
closed
1 year ago
3
GitHub Actions, Python 3.9+ Support, Jupyterlab Extensions
#991
srivarra
closed
1 year ago
3
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