Vizgen/vizgen-postprocessing issues and pull requests

#40 - OpenCV assertion error with combined images

Issue - State: open - Opened by mcmero 3 months ago

#39 - run-segmentation: runtime error (eval() got an unexpected keyword argument 'mask_threshold') and will now exit

Issue - State: closed - Opened by marsdenl 4 months ago - 1 comment

#38 - feat: MERSCOPE Ultra Support

Pull Request - State: closed - Opened by timwiggin 5 months ago

#37 - Python not properly linked

Issue - State: closed - Opened by njohnso6 5 months ago

#36 - Catching empty segmentations (Exception)

Issue - State: open - Opened by pr4deepr 7 months ago

#35 - matplotlib==3.9.0 breaks 'vpt generate-segmentation-metrics'

Issue - State: open - Opened by tangboyun 8 months ago

#34 - chore: Specify version of docker image in workflow

Pull Request - State: closed - Opened by timwiggin about 1 year ago

#33 - chore: Pin sphinx dependencies

Pull Request - State: closed - Opened by timwiggin about 1 year ago

#32 - feat: Support for Cellpose 2 workflow

Pull Request - State: closed - Opened by timwiggin about 1 year ago

#31 - Add an expansion parameter to the cellpose segmentation

Issue - State: open - Opened by sebherbert about 1 year ago

#30 - Quantify the average signal of each channel intensity (protein staining or smFISH) inside each cell boundary after segmentation

Issue - State: open - Opened by wanghlv about 1 year ago

#29 - json "stain" Mismatch

Issue - State: open - Opened by zhenzuo2 about 1 year ago

#28 - .vzg update- runtime error ('Type')

Issue - State: open - Opened by katielong3768 about 1 year ago - 9 comments

#27 - KeyError: Zlevel when importing parquet file generated from baysor polygon geojson

Issue - State: closed - Opened by paularstrpo over 1 year ago - 2 comments

#26 - Convert HDF5 to PARQUET

Issue - State: open - Opened by Byronxy over 1 year ago - 1 comment

#25 - No Fov information in cell_metadata.csv

Issue - State: open - Opened by anidj over 1 year ago - 1 comment

#24 - information relative to the data folder

Issue - State: open - Opened by anidj over 1 year ago

#23 - update-vzg failed with index out of bounds error

Issue - State: open - Opened by tangboyun over 1 year ago

#22 - Invalid value encountered in intersection

Issue - State: closed - Opened by gautam-prab over 1 year ago - 1 comment

#21 - importing segmentation masks

Issue - State: closed - Opened by pr4deepr over 1 year ago - 3 comments

#20 - cannot use custom cellpose model

Issue - State: closed - Opened by pr4deepr over 1 year ago - 3 comments

#19 - feat: Plugin Architecture

Pull Request - State: closed - Opened by timwiggin over 1 year ago

#18 - vpt HPC execution

Issue - State: open - Opened by josemq over 1 year ago - 1 comment

#17 - Polygon units for creating a mask

Issue - State: closed - Opened by pakiessling over 1 year ago

#16 - Custom cell segmentation

Issue - State: open - Opened by vdsukhov over 1 year ago - 2 comments

#15 - Compute the intensity of sequential genes after cell re-segmentation

Issue - State: closed - Opened by Christina-hshi over 1 year ago - 4 comments

#14 - API for assembling experiments

Issue - State: open - Opened by quentinblampey over 1 year ago - 2 comments

#13 - Run-segmentation stops after run-segmentation-on-tile

Issue - State: closed - Opened by pakiessling over 1 year ago - 4 comments

#12 - Using the tool with non-cellpose/watershed segmentation algorithm

Issue - State: closed - Opened by pakiessling over 1 year ago - 2 comments

#11 - How are cell segmented across tiles and z-planes?

Issue - State: closed - Opened by pakiessling almost 2 years ago - 2 comments

#10 - fix: Bug fix for update-vzg temp directory

Pull Request - State: closed - Opened by timwiggin almost 2 years ago

#9 - Meaning of Segmentation fault: 11

Issue - State: open - Opened by munizmom almost 2 years ago - 1 comment

#8 - update-vzg fails when specifying temp-path

Issue - State: open - Opened by jhkliu42 almost 2 years ago - 1 comment

#7 - ValueError: Expected columns {'gene', 'global_z', 'global_x', 'global_y'} were not found in the input-transcripts file.

Issue - State: closed - Opened by mbernste almost 2 years ago - 2 comments

#6 - CellposeSegParameters.init() missing 2 required positional arguments

Issue - State: closed - Opened by mbernste almost 2 years ago - 2 comments

#5 - Unable to install on M1 chip

Issue - State: open - Opened by quentinblampey almost 2 years ago - 3 comments

#4 - unable to run on test dataset

Issue - State: closed - Opened by ucagenomix about 2 years ago - 1 comment

#3 - chore: Remove push to TestPyPI from GHA

Pull Request - State: closed - Opened by timwiggin about 2 years ago

#2 - feat: Initial vpt release

Pull Request - State: closed - Opened by timwiggin about 2 years ago

#1 - Update build command and runner version

Pull Request - State: closed - Opened by timwiggin about 2 years ago

GitHub / Vizgen/vizgen-postprocessing issues and pull requests