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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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Add multiple clustering resolution functionality
#1095
camisowers
closed
4 months ago
2
`IntCastingNaNError` in 3_Pixie_Cluster_Cells notebook
#1094
sarafiller
opened
7 months ago
1
Bump to v0.7.0
#1093
alex-l-kong
closed
7 months ago
0
Generalized masking
#1092
camisowers
closed
2 months ago
3
General signal masking notebook
#1091
camisowers
closed
2 months ago
0
ConnectionResetError when using deepcell_service_utils.create_deepcell_output
#1088
coding0lion
closed
7 months ago
0
2_Pixie_Cluster_Pixel.ipynb not creating pixel_meta_cluster_mapping.csv
#1086
milesbailey121
closed
7 months ago
0
Error with Pixie
#1085
Nitya20001
closed
7 months ago
1
Pixel clustering with Pixie - error
#1084
Nitya20001
closed
7 months ago
0
Fix cell cluster visualization in Mantis
#1083
camisowers
closed
7 months ago
3
Incorrect cell cluster mapping in mantis
#1082
camisowers
closed
7 months ago
2
Speed up pixel clustering for large images
#1081
janinemelsen
closed
7 months ago
4
MIT license
#1080
srivarra
closed
8 months ago
1
`AnnData` Conversion Notebook
#1079
srivarra
closed
7 months ago
2
`AnnData` Conversion Design Document Part 2
#1078
srivarra
closed
7 months ago
3
New License
#1077
srivarra
closed
8 months ago
2
Error when starting Docker with update flag
#1076
cliu72
opened
9 months ago
1
Erosion and size of `plot_pixel_cell_cluster` output
#1075
cliu72
closed
7 months ago
0
Vitessce Integration Design Document
#1074
srivarra
opened
9 months ago
7
AnnData Conversion Design Doc
#1073
srivarra
closed
7 months ago
4
Look into Napari functionality
#1072
ngreenwald
opened
9 months ago
0
Downstream analysis planning
#1071
ngreenwald
opened
9 months ago
0
Add template for generating multiple clustering resolutions
#1070
ngreenwald
closed
4 months ago
0
Allow user to dynamically set batch size of pixel SOM assignments
#1069
alex-l-kong
closed
8 months ago
2
generic cell cluster notebook for nimbus
#1068
HPiyadasa
opened
9 months ago
3
Adustments to Mass Plotting Workflow
#1067
srivarra
closed
9 months ago
1
Mantis viewer export with img_sub_folder = None does not work
#1066
FaehlingT
opened
9 months ago
1
Apply Pixie to Codex dataset
#1065
RYY0722
opened
9 months ago
4
Mass Plotting needs a few adjustments
#1064
srivarra
closed
9 months ago
2
Interactive files
#1063
alex-l-kong
opened
10 months ago
5
norm_vals_name or norm_vals_name_post_rownorm
#1062
FaehlingT
opened
10 months ago
1
Single mantis directory
#1061
camisowers
closed
10 months ago
5
Pin to scikit-image to v0.19.3
#1060
camisowers
closed
10 months ago
2
Single mantis directory
#1059
camisowers
closed
10 months ago
2
Make sure overwrite functionality for pixel clustering propagates into helper functions
#1058
alex-l-kong
closed
10 months ago
2
Apineer v0.1.10
#1057
camisowers
closed
10 months ago
0
Filter FOVs in `calc_distance_matrix`
#1056
srivarra
opened
10 months ago
0
Bad filtering in fiber segmentation
#1055
camisowers
closed
10 months ago
1
Export Clustering results to visualize locally
#1054
FaehlingT
closed
10 months ago
0
Update HuggingFace to main
#1053
alex-l-kong
closed
10 months ago
0
Mass plotting notebook
#1052
srivarra
closed
10 months ago
9
Remove cells that don't have any pixel clusters expressed prior to Pixie
#1051
alex-l-kong
closed
10 months ago
0
Include `img_sub_folder` as parameter in Mantis calls
#1050
alex-l-kong
closed
10 months ago
1
Update README from v0.6.5 to v0.6.6
#1048
alex-l-kong
closed
10 months ago
0
Release 0.6.6 without tables dependency
#1047
alex-l-kong
closed
10 months ago
0
Pixie cell clustering should ignore cells that don't contain any pixel clusters in it
#1046
cliu72
closed
10 months ago
2
Add `img_sub_folder` to `create_mantis_dir` in Pixie
#1045
cliu72
closed
10 months ago
0
"Commercial use" license inquiry
#1044
VictorDidier
closed
10 months ago
2
Fix color_map setting in visualization notebook
#1043
camisowers
closed
10 months ago
0
Update README with Pixie reference
#1042
cliu72
closed
10 months ago
0
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