angelolab ark-analysis issues

angelolab / ark-analysis

Integrated pipeline for multiplexed image analysis

https://ark-analysis.readthedocs.io/en/latest/

MIT License

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issues

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Visualize all markers and cluster names in cell cluster heatmap

#1146 janinemelsen opened 6 days ago
2
Windows Problem With bash start_docker.sh Command

#1145 Nicholas-Bartelo opened 1 week ago
1
Next Release 0.7.1

#1144 srivarra closed 1 week ago
0
module 'ark.phenotyping.post_cluster_utils' has no attribute 'generate_new_cluster_resolution'

#1143 c0urtneyt opened 2 weeks ago
1
Error Running example data in templates/2_Pixie_Cluster_Pixels.ipynb

#1142 mikemcka opened 2 weeks ago
2
"Unassigned" label not included in "population_cell_mask.csv" for Mantis

#1141 cliu72 opened 1 month ago
0
Make row sum normalization optional for pixel-level Pixie preprocessing

#1140 alex-l-kong opened 1 month ago
1
Updated GitHub Workflows

#1139 srivarra closed 2 weeks ago
0
Adjust Github Actions Workflows

#1138 srivarra closed 2 weeks ago
0
`numba` parallelization fault with `relabel_segmentation`

#1137 alex-l-kong opened 2 months ago
0
3_Pixie_Cluster_Cells notebook error. Length mismatch: Expected 5101 rows, received array of length 9931

#1136 fotisn7 closed 2 months ago
2
Error when starting Docker: manifest for angelolab/ark-analysis:v0.7.0 not found

#1135 fotisn7 closed 2 months ago
2
Change python version in conda env file

#1134 srivarra closed 2 months ago
0
2_Pixie_Cluster_Pixels notebook error: cluster_pixels() missing 1 required positional argument: 'pixel_pysom'

#1133 leorrose closed 2 months ago
4
`numpy.distutils` is deprecated

#1132 leorrose closed 2 months ago
2
Merging main into ark_brain_2024 (04/2023)

#1131 bryjcannon closed 2 months ago
1
Fix kmeans notebook mask generation

#1130 camisowers closed 2 months ago
1
generate neighborhood mask results in string error

#1129 janinemelsen closed 2 months ago
1
Fiber stats bugs

#1128 camisowers closed 3 months ago
0
Fix color masking in Pixie

#1127 camisowers closed 3 months ago
1
Manual mask names

#1126 camisowers closed 2 months ago
3
Duplicate FOV name issues with cell table generation

#1125 camisowers closed 2 months ago
0
Don't require user to have all pixel SOM clusters represented during assignment

#1124 alex-l-kong closed 3 months ago
5
1119 reducing time to merge in merge maskspy wi ez segmenter

#1123 bryjcannon closed 3 months ago
1
Allow for a subset of FOVs in k-means clustering notebook

#1122 cliu72 opened 4 months ago
1
ValueError: Lists pixel som weights columns and pixel data columns ordered differently

#1120 janinemelsen closed 4 months ago
1
Reducing time to merge in merge_masks.py w/i ez_segmenter

#1119 bryjcannon closed 3 months ago
1
Pixel Subset in Pixie

#1118 matthew-lee1 closed 4 months ago
5
Error in `plot_utils.save_colored_masks` and `plot.utils.plot_pixel_cell_cluster`

#1117 cliu72 closed 3 months ago
0
Error downloading example dataset

#1116 cliu72 closed 4 months ago
2
Order column pixel_pysom differs from feather file

#1115 janinemelsen closed 4 months ago
0
General CI Updates

#1114 srivarra closed 4 months ago
3
Example Dataset is causing tests to fail

#1113 srivarra closed 4 months ago
0
AnnData spatial analysis 1

#1112 camisowers opened 5 months ago
2
ValueError: pixel_som_clustering.generate_som_avg_files

#1111 dcomimmo closed 3 months ago
18
Don't generate duplicate `cluster_id` columns if `generate_and_save_cluster_masks` run twice

#1110 alex-l-kong closed 4 months ago
0
Generate_cell_table confuses foo1_nuclear and foo10_nuclear

#1109 g-torr closed 4 months ago
1
Remove pixels that were not assigned to cells

#1108 janinemelsen closed 5 months ago
2
Only load whole cell masks if `nuclear_counts=False` in `generate_cell_table`

#1107 alex-l-kong closed 4 months ago
0
Cell clustering unable to parse updated cell table format from `ez_seg` update

#1106 alex-l-kong closed 5 months ago
2
AnnData spatial analysis part 1

#1105 camisowers opened 5 months ago
4
Changes process lists search for matching fov and mask names to use a…

#1104 bryjcannon closed 4 months ago
2
marker_quantification.process_lists() returning inappropriate mask_types

#1103 bryjcannon closed 4 months ago
0
Fix issue with notebook test generators

#1102 alex-l-kong closed 4 months ago
1
1100 empty composites masks in ez segmenter notebook

#1101 bryjcannon closed 4 months ago
2
Empty composites, masks in ez_segmenter notebook.

#1100 bryjcannon closed 4 months ago
0
Error in `create_mantis_dir` in cell clustering notebook if running `generate_and_save_cell_cluster_masks` multiple times

#1099 cliu72 closed 4 months ago
2
Cannot run through example dataset in `3_Pixie_Cluster_Cells.ipynb`

#1098 cliu72 closed 6 months ago
1
Even when setting `nuclear_counts = False`, nuclear masks are being quantified in `marker_quantification.generate_cell_table`

#1097 cliu72 closed 4 months ago
0
FOV names not parsed correctly when running example dataset in `1_Segment_Image_Data.ipynb`

#1096 cliu72 closed 4 months ago
1