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

#251 - Issues with reading in non zarr format Visium HD data in python

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

#249 - In `.geojson` parsed, the index should be parsed from `.geojson`

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

#248 - new test datasets

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

#247 - Visium HD fix bug projective transformation (CytAssist image)

Pull Request - State: open - Opened by LucaMarconato about 2 months ago - 1 comment

#246 - Update README.md

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

#243 - Update MACSima reader when stitching is supported

Issue - State: open - Opened by melonora 2 months ago - 1 comment

#241 - spatialdata_io.xenium error

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

#239 - Add CLI for spatialdata_io.

Pull Request - State: open - Opened by migueLib 3 months ago - 2 comments

#237 - spatialdata-io cant read Xenium data V3

Issue - State: closed - Opened by 2613df 3 months ago

#236 - Import error when loading Xenium data

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

#235 - Missing tiles in Xenium H&E image

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

#234 - Add universal image loader

Pull Request - State: open - Opened by minhtien-trinh 3 months ago - 1 comment

#233 - Add reader for DIA-NN output

Pull Request - State: open - Opened by minhtien-trinh 3 months ago - 1 comment

#232 - import datatree from xarray

Pull Request - State: closed - Opened by melonora 3 months ago - 1 comment

#230 - Detect VisiumHD full-res image when path is relative

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

#229 - Reduce readers' memory consumption

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

#228 - Reduce reader memory consumption

Pull Request - State: open - Opened by marcovarrone 3 months ago - 1 comment

#227 - Update seqfish reader

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

#226 - Remove dummy channel from `xenium`

Issue - State: open - Opened by LucaMarconato 3 months ago
Labels: xenium

#225 - Importing Mass Spec Imaging Data into SpatialData

Issue - State: open - Opened by blakesells7 3 months ago

#224 - add macsima reader

Pull Request - State: closed - Opened by berombau 3 months ago - 1 comment

#222 - to_spatial_image() got an unexpected keyword argument 'rgb'

Issue - State: closed - Opened by yt723 4 months ago - 3 comments

#221 - New Xenium 5K output bundle incompatible with Squidpy

Issue - State: open - Opened by ScienceComputing 5 months ago - 1 comment

#219 - extract shape of full-resolution image, estimate visium pixel size

Pull Request - State: open - Opened by ghaith-mq 4 months ago - 1 comment

#218 - Visium_HD errors

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

#217 - visium_hd() Error

Issue - State: open - Opened by Demond-dev 4 months ago - 2 comments

#216 - Bug in v0.1.5 visium_hd reader

Issue - State: open - Opened by t-a-m-i 4 months ago - 2 comments

#214 - Unable to read Visium HD data

Issue - State: closed - Opened by rreja 4 months ago - 2 comments

#213 - cosmx - ValueError: Affine matrix must be homogeneous.

Issue - State: open - Opened by jamesboot 4 months ago - 7 comments

#212 - Handling empty prefix

Issue - State: open - Opened by hiraksarkar 4 months ago - 4 comments

#211 - Visium hd

Pull Request - State: open - Opened by ArneDefauw 4 months ago - 10 comments

#210 - MERSCOPE: adding feature_key attribute for points

Pull Request - State: closed - Opened by quentinblampey 4 months ago - 2 comments

#209 - create rgb images for visiumhd

Pull Request - State: closed - Opened by melonora 4 months ago - 1 comment

#208 - Merscope - not loading vpt output

Issue - State: open - Opened by MathieuBo 5 months ago - 1 comment

#207 - merscope reader remove invalid polygons

Pull Request - State: open - Opened by ckmah 5 months ago - 3 comments

#206 - change error in warning visium_hd

Pull Request - State: closed - Opened by melonora 5 months ago - 1 comment

#205 - Export the real global coordinates of cells (Xenium)

Issue - State: open - Opened by nkuweili 5 months ago - 1 comment

#204 - adjust for crc2 dataset

Pull Request - State: closed - Opened by melonora 5 months ago - 4 comments

#203 - Confusion on constructing SpatialData object from the ground up

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

#202 - visium_hd: no global coordinate system for image

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

#201 - 3D visualize

Issue - State: open - Opened by Yifan-debug 6 months ago - 1 comment

#200 - Fixes header bug Visium data #146

Pull Request - State: closed - Opened by LucaMarconato 6 months ago - 1 comment

#199 - export visium spot expression to a spatial coordinate matrix

Issue - State: closed - Opened by brainfo 6 months ago - 1 comment

#198 - Xenium: use physical units instead of pixel units as references

Issue - State: open - Opened by wangjiawen2013 6 months ago - 6 comments
Labels: xenium

#197 - Segmented CODEX data in QuPath csv to squidpy

Issue - State: open - Opened by andreevg04 6 months ago - 1 comment

#196 - added dims paramter to xenium_aligned_image()

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

#195 - Can't read re-segmented Xenium data

Issue - State: open - Opened by liz-is 6 months ago - 5 comments
Labels: xenium

#194 - Error importing 10X Visium data

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

#193 - Mappingproxy is not defined

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

#192 - from napari_spatialdata import Interactive - QtBindingsNotFoundError

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

#191 - Disallow points with zero lenght cosmx

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

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

Pull Request - State: open - Opened by pre-commit-ci[bot] 6 months ago

#189 - Handling Missing Transformation Matrices in Visium HD Dataset Loading

Issue - State: closed - Opened by LouisK92 6 months ago - 1 comment

#188 - Xenium cells with 2 nuclei

Issue - State: open - Opened by LucaMarconato 6 months ago
Labels: xenium

#187 - Update README.md

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

#186 - Fix xenium default value and add deprecation warning

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

#185 - Add tifffile to project dependencies

Pull Request - State: closed - Opened by Czaki 6 months ago - 1 comment

#183 - Visium hd bins as squares

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

#181 - Update link to Xenium file format.

Issue - State: open - Opened by LucaMarconato 6 months ago
Labels: xenium

#180 - Verify compatibility with Xenium Onboard Analysis 3.0

Issue - State: open - Opened by LucaMarconato 6 months ago - 1 comment
Labels: xenium

#179 - Fix xenium default instances

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

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

Pull Request - State: closed - Opened by pre-commit-ci[bot] 6 months ago

#177 - Inquiry about Visium HD

Issue - State: open - Opened by aalia09123 6 months ago - 2 comments

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

Pull Request - State: closed - Opened by pre-commit-ci[bot] 6 months ago

#174 - Lack of `tifffile` in project requirements

Issue - State: closed - Opened by Czaki 7 months ago - 1 comment

#172 - fix missing var from_legacy_anndata

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

#171 - Problem with Anndata2SpatialData conversion

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

#170 - Changes to Xenium spec?

Issue - State: closed - Opened by timtreis 7 months ago - 3 comments

#169 - Generate .cloupe file with 2µm bins from Visium HD data

Issue - State: closed - Opened by LucaMarconato 7 months ago - 6 comments

#168 - Alignment image with xenium

Issue - State: open - Opened by Yifan-debug 7 months ago - 24 comments

#167 - Coordinates from Xenium Explorer not matching the original data

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

#165 - adjusted docstrings in steinbock reader py file

Pull Request - State: open - Opened by LukasHats 7 months ago

#164 - fix iss experimental reader

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

#163 - change to get_element_instances

Pull Request - State: closed - Opened by melonora 7 months ago - 1 comment

#162 - Cannot import spatialdata-io in a new conda env

Issue - State: closed - Opened by sunyumail93 8 months ago - 4 comments

#161 - Stereoseq expected directory structure

Issue - State: open - Opened by aadimator 8 months ago - 5 comments

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

Pull Request - State: closed - Opened by pre-commit-ci[bot] 8 months ago

#159 - How to represent rounds and channels in ISS data

Issue - State: open - Opened by tischi 8 months ago - 11 comments

#158 - fix bin_size parsing visium hd

Pull Request - State: closed - Opened by LucaMarconato 8 months ago - 2 comments

#157 - bin_size bug in visium_hd

Issue - State: closed - Opened by alexanderchang1 8 months ago - 1 comment

#156 - [WIP] add macsima reader

Pull Request - State: closed - Opened by berombau 8 months ago - 4 comments

#155 - Support for MACSima data

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

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

Pull Request - State: closed - Opened by pre-commit-ci[bot] 8 months ago

#153 - Fix missing path in codex reader pd.read_csv call

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

#152 - merscope reader update

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