gustaveroussy/sopa issues and pull requests

#182 - [Feature] Allow two separate categories of shapes to be written to Xenium Explorer

Issue - State: open - Opened by pakiessling 17 days ago - 7 comments

#181 - [Feature] Using an existing staining segmentation as a prior for Baysor or ComSeg

Issue - State: closed - Opened by VPetukhov 17 days ago - 6 comments

#180 - [Feature] Clarify how to get the CosMX input

Issue - State: open - Opened by quentinblampey 17 days ago

#179 - ValueError: Invalid dtype int64 for prior cell ids. Must be int or string.

Issue - State: open - Opened by marsdenl 17 days ago - 4 comments

#178 - Sopa2 release candidate

Pull Request - State: closed - Opened by quentinblampey 18 days ago

#177 - [Feature] Custom annotation

Issue - State: closed - Opened by sophiedoublier 23 days ago - 5 comments

#176 - [Bug] sopa write explorer fails after H&E image is added

Issue - State: open - Opened by jpark27 28 days ago - 1 comment

#175 - Add bednarsky updates to sopa2

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

#174 - No common gene when running Tangram in Sopa-CLI model

Issue - State: closed - Opened by KunHHE about 1 month ago - 7 comments

#173 - [Help wanted] --save-h5ad but missed transcript counts

Issue - State: open - Opened by KunHHE about 1 month ago - 2 comments

#172 - multiple samples for spatial analysis using sopa

Issue - State: closed - Opened by KunHHE about 1 month ago

#171 - "niches" from demo data in Spatial statistics section

Issue - State: closed - Opened by KunHHE about 1 month ago - 3 comments

#170 - AnnData h5ad from Scimap output is compatible with the Sopa package for Spatial statistics?

Issue - State: closed - Opened by KunHHE about 2 months ago - 3 comments

#169 - [Bug] Sopa2 error when no cells are found in FOV

Issue - State: closed - Opened by pakiessling about 2 months ago - 7 comments

#168 - [Bug]SpatialData.init() got an unexpected keyword argument 'attrs'

Issue - State: closed - Opened by pakiessling about 2 months ago - 1 comment

#167 - 166 using sopa as module in workflow leads to name error the name paths is unknown in this context

Pull Request - State: closed - Opened by bednarsky about 2 months ago - 2 comments

#166 - Using sopa as module in workflow leads to NameError: The name 'paths' is unknown in this context

Issue - State: closed - Opened by bednarsky about 2 months ago

#165 - [Feature] Sopa2 with BIDcell/segger

Issue - State: open - Opened by jpark27 about 2 months ago - 4 comments

#164 - [Bug] ImportError: cannot import name 'HybridMappingProxy

Issue - State: closed - Opened by NadineBestard about 2 months ago - 1 comment

#163 - reading .hdf5 file in sopa?

Issue - State: open - Opened by KunHHE about 2 months ago - 5 comments

#162 - Writing CosMX segmentation+transcripts to Xenium explorer

Issue - State: closed - Opened by GBeattie 2 months ago - 9 comments

#161 - [help wanted] FileNotFoundError: [Errno 2] No such file or directory for --sopa resolve baysor

Issue - State: closed - Opened by KunHHE 2 months ago - 21 comments

#160 - patch running for Baysor in CLI

Issue - State: closed - Opened by KunHHE 2 months ago - 1 comment

#159 - xarray bump

Pull Request - State: closed - Opened by ArneDefauw 2 months ago - 1 comment

#158 - data reproduce on annotation for sopa paper

Issue - State: closed - Opened by KunHHE 2 months ago - 3 comments

#157 - Patch # has < 4000 transcripts. Segmentation will not be run?

Issue - State: closed - Opened by KunHHE 2 months ago - 2 comments

#157 - Patch # has < 4000 transcripts. Segmentation will not be run?

Issue - State: closed - Opened by KunHHE 2 months ago - 1 comment

#156 - running error on MissingInputException in rule resolve_cellpose for merscope data

Issue - State: closed - Opened by KunHHE 2 months ago - 2 comments

#155 - [Bug] To use cellpose, you need its corresponding sopa extra: `pip install 'sopa[cellpose]`

Issue - State: closed - Opened by juliandwillett 2 months ago - 1 comment

#154 - [Feature] Multiple run of Cellpose/Baysor

Issue - State: open - Opened by lguerard 3 months ago - 6 comments

#154 - [Feature] Multiple run of Cellpose/Baysor

Issue - State: open - Opened by lguerard 3 months ago - 5 comments

#153 - No experiment.xenium file after running `sopa explorer write`

Issue - State: closed - Opened by NJNataren 3 months ago - 1 comment

#153 - No experiment.xenium file after running `sopa explorer write`

Issue - State: closed - Opened by NJNataren 3 months ago - 1 comment

#152 - Issue resolving conflicts with resolve() for Baysor segmentation

Issue - State: open - Opened by NJNataren 3 months ago - 4 comments

#152 - Issue resolving conflicts with resolve() for Baysor segmentation

Issue - State: closed - Opened by NJNataren 3 months ago - 5 comments

#151 - Sopa read issue

Issue - State: closed - Opened by deborahha 3 months ago - 3 comments

#150 - [Feature] Bypass Baysor patches where no cells

Issue - State: closed - Opened by lguerard 3 months ago - 5 comments

#149 - Obtaining transcript confidence and assignment_confidence from baysor segmentation

Issue - State: open - Opened by pngai1 3 months ago - 2 comments

#148 - How to analyze one tissue section data separately from one capture area which include two tissue sections for Xenium 5k ?

Issue - State: open - Opened by lidd77 3 months ago - 1 comment

#147 - Min & Max aggregation methods

Issue - State: closed - Opened by dancelestini 3 months ago - 5 comments
Labels: enhancement

#146 - Sopa read: Could not infer `dataset_id`

Issue - State: closed - Opened by GBeattie 3 months ago - 13 comments

#145 - [Bug] Parallelization backend issues with dask

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

#144 - [Bug] Xenium Prime - empty codewords included in the SOPA output

Issue - State: open - Opened by wlason 3 months ago - 1 comment
Labels: enhancement

#143 - [Bug] Error when writing out tangram annotation mapping

Issue - State: closed - Opened by wlason 4 months ago - 4 comments
Labels: enhancement

#142 - Update config.yaml

Pull Request - State: closed - Opened by wlason 4 months ago - 3 comments

#141 - [Bug] Mistake in slurm config yaml

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

#140 - cherry pick fix for baysor 0.7.0 (#133)

Pull Request - State: closed - Opened by quentinblampey 4 months ago

#139 - [Feature] Allow setting of run_name in sopa explorer write

Issue - State: closed - Opened by pakiessling 4 months ago - 3 comments
Labels: enhancement

#137 - Unable to read a whole slide image into sopa

Issue - State: closed - Opened by asmitaL99 4 months ago - 9 comments

#136 - [Bug] Polygon resolution after cellpose leads to overlapping and misshapen cells

Issue - State: open - Opened by pakiessling 4 months ago - 1 comment

#135 - [Feature] Conda packaging

Issue - State: closed - Opened by lecorguille 4 months ago - 3 comments

#134 - [Bug] Issue with transcripts patches

Issue - State: closed - Opened by lguerard 4 months ago - 4 comments

#133 - KeyError during the process (MERSCOPE)

Issue - State: closed - Opened by ykashima2 4 months ago - 8 comments

#132 - [Feature] Assigning transcript (points) to cells

Issue - State: closed - Opened by pakiessling 4 months ago - 9 comments

#131 - [Bug] Jupyter-lab kernel dying when running segmentation.write_patch_cells

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

#130 - [Feature] Cell Boundary Expansion in DAPI Stained Fluorescence Images

Issue - State: open - Opened by guoyang-github 4 months ago - 4 comments
Labels: enhancement

#129 - [Bug] Issue with dask on branch sopa2

Issue - State: closed - Opened by lguerard 5 months ago - 4 comments

#128 - Dev

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

#127 - Support Baysor>=7.0.0

Pull Request - State: closed - Opened by quentinblampey 5 months ago - 6 comments

#126 - Fix compatibility with latest version of Baysor

Pull Request - State: closed - Opened by lguerard 5 months ago - 6 comments

#125 - [Bug] Issue with new version Baysor

Issue - State: closed - Opened by ykashima2 5 months ago - 6 comments

#124 - Dev

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

#123 - [Bug] Isse with running Baysor segmentation on some but not all patches

Issue - State: open - Opened by marsdenl 5 months ago - 20 comments

#122 - Handling pseudo 3D information

Issue - State: open - Opened by Marius1311 5 months ago - 4 comments

#121 - [Bug] No module named dartie (snakemake)

Issue - State: closed - Opened by marsdenl 5 months ago - 7 comments

#120 - [Feature & Bug] Xenium explorer displaying both Cellpose and Baysor boundaries

Issue - State: closed - Opened by lguerard 5 months ago - 7 comments

#119 - CLI tutorial Baysor segmentation creates different number of patches

Issue - State: closed - Opened by Marius1311 5 months ago - 5 comments

#118 - [Bug] Error in rule patch_segmentation_baysor

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

#117 - [Bug]"Could not find element with name ['cell_circles']"

Issue - State: open - Opened by Yifan-debug 5 months ago - 7 comments

#116 - [Feature] General reader for non-commercial datasets

Issue - State: open - Opened by lopollar 5 months ago - 3 comments

#115 - `sopa.segmentation.transcripts.resolve` for Baysor segmentation fails

Issue - State: closed - Opened by Marius1311 5 months ago - 6 comments

#114 - [Bug]AssertionError: Channel names must be strings, not object

Issue - State: closed - Opened by sunshx-bioinfo 5 months ago - 6 comments

#113 - cell density in sopa.spatial.niches_geometry_stats

Issue - State: closed - Opened by Debohay 6 months ago - 3 comments

#112 - saving masks to png

Issue - State: open - Opened by sunshx-bioinfo 6 months ago - 12 comments

#111 - Dev

Pull Request - State: closed - Opened by quentinblampey 6 months ago

#110 - cell segmentation with only membrane protein

Issue - State: closed - Opened by sunshx-bioinfo 6 months ago - 9 comments

#109 - cell segmentation strategy

Issue - State: closed - Opened by wangjiawen2013 6 months ago - 2 comments

#108 - Dev

Pull Request - State: closed - Opened by quentinblampey 6 months ago

#107 - [Bug]Invalid element type: <class 'xarray.core.dataarray.DataArray'>

Issue - State: closed - Opened by Yifan-debug 6 months ago - 3 comments

#106 - [Bug]ArrowInvalid: Parquet magic bytes not found in footer. Either the file is corrupted or this is not a parquet file.

Issue - State: closed - Opened by Yifan-debug 6 months ago - 2 comments

#105 - Issue with Reproducing Xenium V1 Data Using SOPA v1.1.12

Issue - State: closed - Opened by bhyu0217 6 months ago - 5 comments

#104 - [Bug] Morphology.ome.tif low resolution after running Sopa on Xenium Sample

Issue - State: closed - Opened by pakiessling 6 months ago - 4 comments

#103 - Scaling sopa to run many images

Issue - State: open - Opened by josenimo 6 months ago - 5 comments

#102 - Crop Feature for API users

Issue - State: closed - Opened by marsdenl 6 months ago - 2 comments

#101 - [Bug] Aggregator.compute_table raises ValueError: negative axis 1 index: -1

Issue - State: closed - Opened by pakiessling 6 months ago - 6 comments

#100 - Dev

Pull Request - State: closed - Opened by quentinblampey 6 months ago

#99 - Passing kwargs to cellpose from yaml

Issue - State: closed - Opened by pakiessling 6 months ago - 2 comments

#98 - [Feature] Quantile projection for cyto3 segmentation

Issue - State: closed - Opened by josenimo 7 months ago - 2 comments

#97 - Dev

Pull Request - State: closed - Opened by quentinblampey 7 months ago

#96 - Incompatible coordinate transformation with cellpose segmentation result

Issue - State: open - Opened by mamyAndrianteranagna 7 months ago - 14 comments

GitHub / gustaveroussy/sopa issues and pull requests