Ecosyste.ms: Issues

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

GitHub / scverse/spatialdata-io issues and pull requests

#151 - Made Xenium table optional

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

#150 - Error to read in Baysor segmented Xenium data

Issue - State: closed - Opened by Bo-UT 8 months ago - 1 comment

#149 - Support for `binned_ouputs` folder for Visium HD

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

#148 - update codecov

Pull Request - State: closed - Opened by giovp 8 months ago - 1 comment

#147 - Wrong file loaded when building new SpatialData

Issue - State: open - Opened by dawe 9 months ago - 2 comments

#145 - Error when trying to import Visium HD data

Issue - State: closed - Opened by alexanderchang1 9 months ago - 18 comments

#144 - Converting VisiumHD to .zarr

Issue - State: closed - Opened by RijndertAriese 9 months ago

#143 - visium HD doesn't have "filtered" counts file but "slice_file"

Issue - State: closed - Opened by giovp 9 months ago - 1 comment

#142 - Xenium test datasets

Pull Request - State: closed - Opened by LucaMarconato 9 months ago - 4 comments

#141 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 9 months ago

#140 - Cannot load VisiumHD data without image

Issue - State: open - Opened by pakiessling 9 months ago

#139 - Fixed path searching behavior in DBiT reader.

Pull Request - State: closed - Opened by lillux 9 months ago - 4 comments

#138 - store probe set for image-based transcriptomics in spatialdata

Issue - State: open - Opened by giovp 9 months ago - 3 comments

#137 - CosMX reader with stitching

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

#135 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 10 months ago

#134 - experimental.to_legacy_anndata fails when no global image is provided

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

#133 - make obs names unique

Pull Request - State: closed - Opened by melonora 10 months ago - 5 comments

#132 - error from minimalistic reading of xenium data

Issue - State: closed - Opened by EliHei2 10 months ago - 4 comments

#131 - fix docs and tests

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

#130 - Visium HD support

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

#129 - Cannot open example data files with current spatialdata

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

#128 - Update release.yaml

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

#127 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 10 months ago - 1 comment

#126 - Update test_and_deploy.yaml

Pull Request - State: closed - Opened by LucaMarconato 11 months ago - 2 comments

#125 - Multi table

Pull Request - State: closed - Opened by melonora 11 months ago - 2 comments

#124 - Wrong Visium radii?

Issue - State: open - Opened by LucaMarconato 11 months ago - 1 comment

#123 - Consider using nuclei locations for Xenium data when `cells_as_circles` is `True`

Issue - State: closed - Opened by LucaMarconato 11 months ago - 1 comment
Labels: xenium

#122 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 11 months ago

#121 - High RAM usage with the MERSCOPE reader

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

#120 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 11 months ago

#119 - fixed visium image shape parsing

Pull Request - State: closed - Opened by LucaMarconato 11 months ago - 1 comment

#118 - Xenium: error `unhashable type: 'list'`

Issue - State: closed - Opened by EST09 11 months ago - 1 comment

#117 - Empty color values in images after polygon_query from Xenium data

Issue - State: closed - Opened by Bo-UT 11 months ago - 11 comments

#116 - Update mcmicro

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

#115 - Fixed inplace barcode coordinate sorting in dbit reader

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

#114 - Sorting in place causes misalignment of all data

Issue - State: closed - Opened by dawe 11 months ago - 1 comment

#113 - Dbit reader - improved barcode checking behavior

Pull Request - State: closed - Opened by lillux 11 months ago - 2 comments

#112 - Support for `cells.zarr.zip` for Xenium

Pull Request - State: closed - Opened by LucaMarconato 12 months ago - 3 comments

#111 - Support for xenium analyzer 2.0.0

Pull Request - State: closed - Opened by LucaMarconato 12 months ago - 3 comments

#110 - Support `cells.zarr.zip` for Xenium data

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

#109 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 12 months ago - 1 comment

#108 - Links to third-party readers

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

#107 - visium supports raw reads

Pull Request - State: closed - Opened by LucaMarconato 12 months ago - 2 comments

#106 - Read xenium explorer selection

Pull Request - State: closed - Opened by quentinblampey 12 months ago - 8 comments

#105 - Read xenium explorer selection

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

#104 - `spatialdata_io.visium` Drops Non-Tissue Spots

Issue - State: closed - Opened by jeffquinn-msk almost 1 year ago - 4 comments

#103 - spatialdata_io.xenium xarray chunk error when morphology_focus = True

Issue - State: closed - Opened by pakiessling about 1 year ago - 5 comments

#102 - Add function to export spatialdata to legacy anndata format

Pull Request - State: closed - Opened by grst about 1 year ago - 9 comments

#101 - Axes flipped when reading in Visium data

Issue - State: closed - Opened by grst about 1 year ago - 12 comments

#100 - Post-Xenium images support

Pull Request - State: closed - Opened by LucaMarconato about 1 year ago - 3 comments

#99 - importing cellcharter

Issue - State: closed - Opened by SBDixit about 1 year ago - 1 comment

#98 - Fix xenium index

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

#97 - Improvements for Stereoseq reader

Issue - State: closed - Opened by florianingelfinger about 1 year ago - 9 comments

#96 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] about 1 year ago - 1 comment

#95 - Dbit

Pull Request - State: closed - Opened by lillux about 1 year ago - 9 comments

#94 - fix visium axes ordering for many versions AND cytassist.

Pull Request - State: closed - Opened by giovp about 1 year ago - 2 comments

#93 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] about 1 year ago - 2 comments

#92 - Issues loading any image

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

#91 - Fixed visium() to support file counts without dataset_id

Pull Request - State: closed - Opened by LucaMarconato over 1 year ago - 4 comments

#89 - issue loading MERSCOPE results

Issue - State: closed - Opened by mkunst23 over 1 year ago - 7 comments
Labels: needs info

#88 - problem loading MERSCOPE data

Issue - State: closed - Opened by mkunst23 over 1 year ago - 1 comment

#87 - MERSCOPE: don't try to load unexisting elements

Pull Request - State: closed - Opened by quentinblampey over 1 year ago - 6 comments

#86 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 1 year ago - 1 comment

#85 - Nanostring TileDB export, new format

Issue - State: open - Opened by mkattah over 1 year ago - 3 comments

#84 - add osmfish

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

#83 - updated changelog files

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

#82 - Reading external segmentation results

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

#81 - Fix xenium string decode bug

Pull Request - State: closed - Opened by callum-jpg over 1 year ago - 1 comment

#80 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 1 year ago - 1 comment

#79 - Cannot read our new Xenium dataset

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

#78 - Set rgb argument to auto-detect whether image channels are RGB

Pull Request - State: closed - Opened by aeisenbarth over 1 year ago - 4 comments

#77 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 1 year ago

#76 - Issues with reading 10X VISIUM Cytassist data SpaceRanger Output

Issue - State: closed - Opened by thjimmylee over 1 year ago - 6 comments

#75 - Added ISS support of Sanger data format

Pull Request - State: closed - Opened by BioinfoTongLI over 1 year ago - 12 comments

#74 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 1 year ago - 1 comment

#73 - Improvements/fixes: merscope reader

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

#72 - Added first simple version of CLI script.

Pull Request - State: open - Opened by FloWuenne over 1 year ago - 2 comments

#71 - How to load Merscope data missing cell_boundaries.parquet file?

Issue - State: open - Opened by ghar1821 over 1 year ago - 6 comments

#70 - Add reader for Stereo-seq files.

Pull Request - State: closed - Opened by LLehner over 1 year ago - 14 comments

#69 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 1 year ago

#68 - fix coordinate transformation

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

#67 - Failed Xenium Write

Issue - State: closed - Opened by virpatel524 over 1 year ago - 4 comments

#66 - API for reading in raw MCD files from IMC experiments

Issue - State: open - Opened by matt-sd-watson over 1 year ago - 1 comment

#65 - Problem reading standard Xenium datasets

Issue - State: closed - Opened by EliHei2 over 1 year ago - 3 comments

#64 - Coerce cell id to str

Pull Request - State: closed - Opened by melonora over 1 year ago - 2 comments

#63 - Xenium IO AssertionError

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

#62 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 1 year ago - 1 comment

#61 - `read_fcs` not in requirements

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

#60 - Fix key type in CODEX reader

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

#59 - minor fix visium logging

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

#58 - Fix CODEX reader

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

#57 - Update docs

Pull Request - State: closed - Opened by LLehner over 1 year ago - 2 comments

#56 - Fix xenium reader bugs: MORPHOLOGY_FOCUS_FILE and array_assert

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

#55 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 1 year ago

#54 - Fix coordinates in Xenium reader

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

#53 - Reader for seqFISH data

Pull Request - State: closed - Opened by LLehner over 1 year ago - 11 comments

#52 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 1 year ago