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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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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
Investigate distributions of cell statistics
#990
ngreenwald
closed
1 year ago
0
Cell neigborhood diversity
#989
camisowers
closed
1 year ago
2
Initial commit of phenotype by neighbour analysis
#988
khoulahan
closed
1 year ago
1
Lists cell counts cluster ids and pixel channel cluster ids ordered differently
#986
zsfrbkv
closed
1 year ago
3
Add channel normalization and pixel thresholding back
#985
alex-l-kong
closed
1 year ago
5
Skip spatial LDA visualization tests due to Numpy error
#984
alex-l-kong
closed
1 year ago
0
Fix pixel and cell cluster mask generation index for rectangular images
#983
alex-l-kong
closed
1 year ago
2
Diversity of the neighborhood around a given cell
#982
ngreenwald
closed
1 year ago
0
Mutiple tiled stitching tweaks
#981
camisowers
closed
1 year ago
7
Re-add channel normalization and pixel thresholding to Pixie
#980
alex-l-kong
closed
1 year ago
7
Error during installation of pyFlowSom
#979
genomelab
closed
1 year ago
1
Kmeans plotting cell border fix
#978
camisowers
closed
1 year ago
0
Set Kmeans parameter to prior default
#977
camisowers
closed
1 year ago
0
:arrow_up: Bump pypa/cibuildwheel from 2.11.4 to 2.12.3
#976
dependabot[bot]
closed
1 year ago
1
Alpineer updates causing tiled stitching errors
#975
camisowers
closed
1 year ago
0
Downstream fiber analysis updates
#974
camisowers
closed
1 year ago
2
Extended Attributes on macOS
#973
srivarra
closed
1 year ago
2
2 identicle pixel cluster names causes error when running train_cell_som
#972
HPiyadasa
closed
1 year ago
6
List empty directories for `generate_cell_table` as additional debugging
#971
alex-l-kong
closed
1 year ago
0
Progress bar in create_deepcell_output function behaviour
#970
HPiyadasa
closed
1 year ago
0
`create_mantis_dir` breaks if there is no segmentation directory
#969
cliu72
closed
1 year ago
0
Potential bug in neighborhood assignments
#968
ngreenwald
closed
1 year ago
4
plot_neighborhood_cluster_result has multiple colors per cell
#967
ngreenwald
closed
1 year ago
1
Kmeans notebook minor fixes
#966
camisowers
closed
1 year ago
1
Document supported python versions, expand versions
#965
ngreenwald
closed
1 year ago
1
Draw heatmap doesn't save plots correctly
#964
ngreenwald
closed
1 year ago
1
Neighborhood analysis notebook doesn't pass correct cell column
#963
ngreenwald
closed
1 year ago
1
Training Pixel SOM: Segmentation error (core dumped)
#962
Pacomito
closed
1 year ago
5
Update citation information
#961
ngreenwald
closed
1 year ago
0
Next Release v0.6.3
#960
srivarra
closed
1 year ago
0
Next Release - v0.6.2
#959
srivarra
closed
1 year ago
0
ezSegmentation
#958
srivarra
closed
9 months ago
3
Add pip install instructions to README
#957
cliu72
closed
1 year ago
0
Fix zero pixels
#956
cliu72
closed
1 year ago
0
Next Release `v0.6.1`
#955
srivarra
closed
1 year ago
0
Unpin `ipywidgets` in the future
#954
srivarra
closed
1 year ago
0
Pinned `ipywidgets`
#953
srivarra
closed
1 year ago
1
Metaclustering `DEBUG_VIEW` gives a cryptic error on the latest version of `ipywidgets` (8.0.5)
#952
srivarra
closed
1 year ago
0
Change os.rename to shutil.move
#951
cliu72
closed
1 year ago
0
Deprecate use of cluster, metacluster, and mc_name outside of remapping
#950
alex-l-kong
closed
1 year ago
3
Remove extra files
#949
cliu72
closed
1 year ago
2
For `docker.yml` checkout the tag used in `pypi_publish`
#948
srivarra
closed
1 year ago
2
Docker Workflow checks out `main` instead of a tagged branch
#947
srivarra
closed
1 year ago
0
Kmeans notebook cleanup
#946
camisowers
closed
1 year ago
2
Next Release - v0.6.0
#945
alex-l-kong
closed
1 year ago
0
Next Release - v0.5.3
#944
alex-l-kong
closed
1 year ago
0
:arrow_up: Bump pypa/cibuildwheel from 2.11.4 to 2.12.1
#943
dependabot[bot]
closed
1 year ago
1
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