Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / gustaveroussy/sopa issues and pull requests

#85 - [Bug] ValueError: Invalid element type: <class 'datatree.datatree.DataTree'>

Issue - State: closed - Opened by josenimo 7 months ago - 10 comments

#84 - snakemake executes wrong rule

Issue - State: open - Opened by xiao233333 7 months ago - 1 comment

#83 - Classifying positive cells

Issue - State: closed - Opened by dylanmr 8 months ago - 7 comments

#82 - Dev

Pull Request - State: closed - Opened by quentinblampey 8 months ago

#81 - Advice on simple IF hystocytometry

Issue - State: closed - Opened by cstrlln 8 months ago - 11 comments

#79 - Filtering by qv score for Xenium datasets

Issue - State: closed - Opened by saito-k1 8 months ago - 3 comments

#78 - Immunofluorescence Image Segmentation

Issue - State: open - Opened by suhridbuddha 8 months ago - 1 comment

#78 - Immunofluorescence Image Segmentation

Issue - State: open - Opened by suhridbuddha 8 months ago - 1 comment

#77 - Two questions about the Baysor pipeline

Issue - State: closed - Opened by pakiessling 8 months ago - 5 comments

#77 - Two questions about the Baysor pipeline

Issue - State: closed - Opened by pakiessling 8 months ago - 5 comments

#76 - Comseg cli

Pull Request - State: closed - Opened by tdefa 8 months ago - 7 comments

#74 - comseg_patch update and api_tuto"

Pull Request - State: closed - Opened by tdefa 8 months ago

#73 - Visium HD support

Issue - State: closed - Opened by quentinblampey 8 months ago - 2 comments

#72 - Dev

Pull Request - State: closed - Opened by stergioc 9 months ago

#71 - WSI tile gathering optimizations

Pull Request - State: closed - Opened by stergioc 9 months ago

#70 - WSI processing updates

Pull Request - State: closed - Opened by stergioc 9 months ago - 1 comment

#69 - Dev

Pull Request - State: closed - Opened by quentinblampey 9 months ago

#68 - Xenium Input File Change

Issue - State: closed - Opened by saito-k1 9 months ago - 6 comments

#67 - [advice]Cellpose troubleshooting

Issue - State: closed - Opened by cstrlln 9 months ago - 3 comments

#66 - Dev

Pull Request - State: closed - Opened by quentinblampey 9 months ago

#65 - snakemake pipeline on subset of FOVs

Issue - State: closed - Opened by cstrlln 9 months ago - 18 comments

#64 - sdata object has no cellpose or baysor boundaries

Issue - State: closed - Opened by altunbulakli 9 months ago - 21 comments

#63 - CosMx input file format requirements

Issue - State: closed - Opened by Jwong684 9 months ago - 12 comments

#62 - [Feature] how to handle updated output from different technologies.

Issue - State: closed - Opened by cstrlln 9 months ago - 5 comments

#61 - [help wanted] Other segmentation options

Issue - State: closed - Opened by cstrlln 9 months ago - 7 comments

#60 - Dev

Pull Request - State: closed - Opened by quentinblampey 10 months ago

#59 - [Feature] Cellpose - artificially define an area of cytoplasm

Issue - State: closed - Opened by mariavigovaldoleiros 10 months ago - 4 comments

#58 - [Feature] Use .CZI data in SOPA

Issue - State: closed - Opened by mariavigovaldoleiros 10 months ago - 3 comments

#57 - Add patch embeddings with overlaps

Issue - State: closed - Opened by stergioc 10 months ago - 1 comment

#56 - overlay segmentation #55

Pull Request - State: closed - Opened by quentinblampey 10 months ago

#55 - Overlay custom segmentation using cell segmentation resolver

Issue - State: closed - Opened by EST09 10 months ago - 13 comments

#54 - use double quotes in cli #49

Pull Request - State: closed - Opened by quentinblampey 10 months ago

#53 - pin python 3.11 version in ci

Pull Request - State: closed - Opened by quentinblampey 10 months ago

#52 - Dev

Pull Request - State: closed - Opened by quentinblampey 10 months ago

#51 - Adds openslide backend

Pull Request - State: closed - Opened by stergioc 10 months ago - 1 comment

#50 - Dev

Pull Request - State: closed - Opened by quentinblampey 10 months ago

#49 - Vizgen-merscope

Issue - State: closed - Opened by HSvitina 10 months ago - 10 comments

#48 - Questions about Spatial Statistics Analysis

Issue - State: closed - Opened by wikk-chy 10 months ago - 4 comments

#47 - cell id corresponds

Issue - State: closed - Opened by Chuang1118 10 months ago - 6 comments

#46 - support multi-tables

Pull Request - State: closed - Opened by quentinblampey 10 months ago

#45 - hotfix v1.0.8

Pull Request - State: closed - Opened by quentinblampey 10 months ago

#44 - upstream analysis

Issue - State: closed - Opened by rocketeer1998 10 months ago - 6 comments

#41 - [Bug] Baysor fails when too few transcripts

Issue - State: closed - Opened by quentinblampey 11 months ago - 3 comments

#40 - Merge v1.0.7

Pull Request - State: closed - Opened by quentinblampey 11 months ago

#39 - pip install

Issue - State: closed - Opened by HSvitina 11 months ago - 2 comments

#38 - Where is the tuto.zarr from the tuto.zarr?

Issue - State: closed - Opened by suhridbuddha 11 months ago - 4 comments

#35 - CLI patching and cellpose segmentation + GPU

Issue - State: closed - Opened by andrea-de-micheli 11 months ago - 16 comments

#34 - Dev

Pull Request - State: closed - Opened by quentinblampey 11 months ago

#33 - Dev

Pull Request - State: closed - Opened by quentinblampey 11 months ago

#32 - Memory/RAM issue when writing MERSCOPE data (sopa read)

Issue - State: closed - Opened by andrea-de-micheli 11 months ago - 10 comments

#31 - Dev

Pull Request - State: closed - Opened by quentinblampey 11 months ago

#30 - v1.0.5

Pull Request - State: closed - Opened by quentinblampey 11 months ago

#29 - Speeding up Sopa explorer write

Issue - State: closed - Opened by pakiessling 12 months ago - 18 comments

#27 - Merge v1.0.4

Pull Request - State: closed - Opened by quentinblampey 12 months ago

#26 - Adding patch embeddings

Pull Request - State: closed - Opened by stergioc 12 months ago - 11 comments

#25 - CellViT Implementation

Pull Request - State: closed - Opened by loic-lb 12 months ago - 1 comment

#24 - version 1.0.3

Pull Request - State: closed - Opened by quentinblampey 12 months ago

#23 - [Bug] AssertionError during Baysor `patchify_transcripts`

Issue - State: closed - Opened by quentinblampey 12 months ago - 1 comment

#22 - Test new CI

Pull Request - State: closed - Opened by quentinblampey 12 months ago - 1 comment

#21 - WSI I/O and Tissue Segmentation with Otsu

Pull Request - State: closed - Opened by stergioc 12 months ago - 9 comments

#20 - [Bug] Zero count on resolved cells after Baysor

Issue - State: closed - Opened by quentinblampey about 1 year ago - 3 comments

#19 - [Feature] Support WSI analysis

Issue - State: closed - Opened by quentinblampey about 1 year ago - 8 comments

#18 - [Feature] Save both nucleus + cytoplasm boundaries

Issue - State: closed - Opened by quentinblampey about 1 year ago - 1 comment
Labels: enhancement

#17 - [Bug] baysor jobs fail with DomainError

Issue - State: closed - Opened by pakiessling about 1 year ago - 3 comments

#16 - Dev

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

#15 - Suggestions for documentation

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

#14 - [Bug] Error in to_spatialdata , Snakemake + Slurm

Issue - State: closed - Opened by pakiessling about 1 year ago - 3 comments

#13 - run Baysor using cellpose segmentation as prior

Issue - State: closed - Opened by giuliabarbiera about 1 year ago - 7 comments

#11 - [Bug] Self-intersection in resolve conflict (TopologyException)

Issue - State: closed - Opened by quentinblampey about 1 year ago - 1 comment
Labels: bug

#10 - Error running snakemake

Issue - State: closed - Opened by justinesjw about 1 year ago - 5 comments
Labels: bug

#9 - Steps to use APIs

Issue - State: closed - Opened by justinesjw about 1 year ago - 6 comments
Labels: documentation

#9 - Steps to use APIs

Issue - State: open - Opened by justinesjw about 1 year ago - 2 comments

#8 - [Feature] Multiple segmentation rounds of stains or cells + nuclei

Issue - State: closed - Opened by pakiessling about 1 year ago - 7 comments
Labels: enhancement

#7 - Add nextflow pipeline

Issue - State: open - Opened by quentinblampey about 1 year ago - 2 comments
Labels: enhancement, help wanted

#6 - Clean up snakemake temporary files

Issue - State: closed - Opened by quentinblampey over 1 year ago - 1 comment
Labels: enhancement

#5 - CosMX stitching images

Issue - State: closed - Opened by quentinblampey over 1 year ago - 1 comment
Labels: enhancement

#4 - Brighter images in the explorer

Issue - State: closed - Opened by quentinblampey over 1 year ago - 1 comment
Labels: enhancement

#3 - Faster spatial statistics

Issue - State: closed - Opened by quentinblampey over 1 year ago - 1 comment
Labels: enhancement

#2 - Add pipeline HTML report

Issue - State: closed - Opened by quentinblampey over 1 year ago
Labels: enhancement

#1 - Writing transcripts to explorer: using Dask

Issue - State: closed - Opened by quentinblampey over 1 year ago - 1 comment
Labels: enhancement