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34 Open 539 Closed
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Issues list

Tips for Handling Large High-Resolution Tiff Images with Multiple Channels in the arc-analysis Pipeline question Further information is requested
#1178 opened Jan 10, 2025 by vyshakha
Noise in Tiff Image Processing (Non-zero Values in Empty Regions Affecting Marker Expression Analysis) question Further information is requested
#1177 opened Jan 10, 2025 by vyshakha
Heatmap used for manual cluster adjustment in 3_Pixie_Cluster_Cells does no match the cell phenotype mask bug Something isn't working
#1176 opened Dec 16, 2024 by rach-crc
8
Convert Pixie to AnnData design_doc Detailed implementation plan
#1174 opened Nov 7, 2024 by alex-l-kong
1 of 3 tasks
@alex-l-kong
3
Nuclear signal not being size normalized when generating cell table bug Something isn't working help wanted Extra attention is needed
#1171 opened Oct 30, 2024 by alex-l-kong
1
Functional markers enhancement New feature or request
#1170 opened Oct 21, 2024 by smith6jt-cop
3
Neighborhood matrix ValueError: did not find a match in any of xarray's currently installed IO backends ['scipy', 'zarr']. bug Something isn't working
#1169 opened Oct 11, 2024 by smith6jt-cop v0.8.0 Release
2
Update scikit-image / Fiber Segmentation dependencies Pull requests that update a dependency file enhancement New feature or request
#1162 opened Oct 4, 2024 by srivarra v0.8.0 Release
[v0.8.0] Additional Enhancements
#1160 opened Oct 3, 2024 by srivarra
3 of 7 tasks
v0.8.0 Release
OME-TIFF to single channel workflow fails if metadata not contained bug Something isn't working
#1155 opened Sep 17, 2024 by alex-l-kong v0.8.0 Release
Allow option to turn off numba parallelization bug Something isn't working
#1153 opened Sep 3, 2024 by alex-l-kong v0.8.0 Release
Visualize all markers and cluster names in cell cluster heatmap question Further information is requested
#1146 opened Jul 1, 2024 by janinemelsen
1
2
module 'ark.phenotyping.post_cluster_utils' has no attribute 'generate_new_cluster_resolution' question Further information is requested
#1143 opened Jun 19, 2024 by c0urtneyt v0.8.0 Release
1
"Unassigned" label not included in "population_cell_mask.csv" for Mantis bug Something isn't working
#1141 opened May 28, 2024 by cliu72 v0.8.0 Release
numba parallelization fault with relabel_segmentation bug Something isn't working
#1137 opened Apr 23, 2024 by alex-l-kong v0.8.0 Release
Allow for a subset of FOVs in k-means clustering notebook bug Something isn't working
#1122 opened Mar 7, 2024 by cliu72
@camisowers
1
AnnData spatial analysis part 1 design_doc Detailed implementation plan
#1105 opened Jan 10, 2024 by camisowers
1 of 3 tasks
1
@camisowers
4
IntCastingNaNError in 3_Pixie_Cluster_Cells notebook question Further information is requested
#1094 opened Dec 8, 2023 by sarafiller
1
Error when starting Docker with update flag bug Something isn't working
#1076 opened Oct 13, 2023 by cliu72 v0.8.0 Release
1
Vitessce Integration Design Document design_doc Detailed implementation plan
#1074 opened Oct 10, 2023 by srivarra
7
Look into Napari functionality enhancement New feature or request
#1072 opened Oct 3, 2023 by ngreenwald
@srivarra
Downstream analysis planning design_doc Detailed implementation plan enhancement New feature or request
#1071 opened Sep 29, 2023 by ngreenwald
generic cell cluster notebook for nimbus enhancement New feature or request
#1068 opened Sep 28, 2023 by HPiyadasa
3
Mantis viewer export with img_sub_folder = None does not work bug Something isn't working
#1066 opened Sep 27, 2023 by FaehlingT
1
Apply Pixie to Codex dataset question Further information is requested
#1065 opened Sep 24, 2023 by RYY0722
4
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