scverse/squidpy issues and pull requests

#905 - Extend monkeybread neighbourhood to include n>1 cells

Issue - State: open - Opened by timtreis 19 days ago
Labels: enhancement :sparkles:, graph :spider_web:, feature, squidpy2.0

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

Pull Request - State: closed - Opened by pre-commit-ci[bot] 20 days ago

#903 - numpy 2.0 and python >= 3.10 compatibility changes

Pull Request - State: open - Opened by timtreis 26 days ago

#902 - Numpy 2 Compat

Issue - State: open - Opened by ilan-gold about 1 month ago

#901 - Add SpaGFT-like method for identification of SVGs

Issue - State: open - Opened by timtreis about 1 month ago
Labels: enhancement :sparkles:, graph :spider_web:, squidpy2.0

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

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

#899 - How to draw co_occurrence plot with specific distance in x-axis?

Issue - State: open - Opened by Zhaowado about 1 month ago

#898 - Sparse matrix fix

Pull Request - State: closed - Opened by alam-shahul about 1 month ago - 1 comment

#897 - How to combine the image from ImageCollection object with a anndata object?

Issue - State: closed - Opened by HelloWorldLTY about 1 month ago - 4 comments

#896 - Update .pre-commit-config.yaml

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

#895 - How to save the iamge as svs or png?

Issue - State: closed - Opened by HelloWorldLTY about 1 month ago - 1 comment

#894 - CosMx FOVs being skipped

Issue - State: open - Opened by jamesboot about 2 months ago

#893 - Tutorial for Visium applicable to Visium HD?

Issue - State: closed - Opened by spatts14 about 2 months ago - 3 comments

#892 - `TypeError` when going through the Visium tutorial

Issue - State: closed - Opened by matt-sd-watson about 2 months ago - 1 comment

#891 - Fix sparse matrix interactions in `sq.gr.utils`.

Pull Request - State: closed - Opened by alam-shahul about 2 months ago - 3 comments

#890 - `squidpy==1.6.1` not compatible with `anndata>=0.11.0`

Issue - State: closed - Opened by alam-shahul about 2 months ago

#889 - Mapping of Xenium 5k data

Issue - State: open - Opened by shanggutianzhen 2 months ago - 5 comments
Labels: I/O :cd:

#888 - is there a way to view older versions of the documentation over on readthedocs?

Issue - State: closed - Opened by owenwilkins 2 months ago - 3 comments
Labels: doc

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

Issue - State: open - Opened by ScienceComputing 2 months ago
Labels: I/O :cd:

#886 - Edge correction in `squidpy.gr.ripley`?

Issue - State: open - Opened by zsfrbkv 2 months ago - 1 comment
Labels: enhancement :sparkles:, graph :spider_web:

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

Pull Request - State: closed - Opened by pre-commit-ci[bot] 2 months ago

#884 - [doc improvment] inconsistent usage of img_key and img_res_key in code base

Issue - State: open - Opened by TTTPOB 3 months ago - 1 comment
Labels: doc

#883 - add release note

Pull Request - State: closed - Opened by giovp 3 months ago

#882 - remove 3.9 support, fix precommit, release note

Pull Request - State: closed - Opened by giovp 3 months ago

#881 - fix precommit

Pull Request - State: closed - Opened by giovp 3 months ago

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

Pull Request - State: closed - Opened by pre-commit-ci[bot] 3 months ago

#879 - Add SpatialLeiden as clustering method

Issue - State: open - Opened by timtreis 3 months ago
Labels: enhancement :sparkles:, graph :spider_web:

#878 - Expected Width error calculate_image_features

Issue - State: closed - Opened by qiutip 3 months ago

#877 - remove napari from install

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

#876 - Infer parameters in `sq.gr.spatial_neighbors` when only one choice

Issue - State: open - Opened by timtreis 3 months ago - 1 comment
Labels: enhancement :sparkles:, graph :spider_web:, sdata compat :milky_way:

#875 - Catch-all: XYZ doesn't work with `SpatialData`

Issue - State: open - Opened by timtreis 3 months ago - 4 comments
Labels: enhancement :sparkles:, squidpy2.0, sdata compat :milky_way:

#874 - Incompatibility with spatialdata objects on plotting features by using sq.pl.spatial_scatter

Issue - State: closed - Opened by joonlee3 3 months ago - 1 comment
Labels: plot :hibiscus:

#873 - Is Xenium data can be 3D visualization/ can the Stardist do 3D segmentation/ is squidy able to crop image for further analysis

Issue - State: closed - Opened by Yifan-debug 3 months ago - 2 comments
Labels: question :question:, image :microscope:

#872 - Import from QuPath or CODEX Dataset

Issue - State: open - Opened by andreevg04 3 months ago - 1 comment
Labels: question :question:

#871 - Ligand-receptor plot always report Error

Issue - State: open - Opened by ryrl970311 3 months ago - 5 comments
Labels: bug :bug:

#870 - sq.gr.ripley() cost too much memory

Issue - State: open - Opened by wangjiawen2013 3 months ago - 1 comment
Labels: enhancement :sparkles:, graph :spider_web:, speed up :runner:

#869 - Fix links to references

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

#868 - Update ```var_by_distance```

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

#867 - No matching definition for argument type

Issue - State: open - Opened by wangjiawen2013 3 months ago - 3 comments

#866 - MVP for morpohology module

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

#865 - `_pickle.UnpicklingError: pickle data was truncated` running ligrec

Issue - State: closed - Opened by Rafael-Silva-Oliveira 3 months ago - 1 comment

#864 - quick fix to ```var_by_distance```

Issue - State: closed - Opened by LLehner 3 months ago
Labels: enhancement :sparkles:

#863 - CosMx sq.pl.spatial_segment() error: buffer source array is read-only

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

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

Pull Request - State: closed - Opened by pre-commit-ci[bot] 4 months ago - 1 comment

#861 - Working on 3D segmentation matrix

Issue - State: open - Opened by rsemeraro 4 months ago - 2 comments
Labels: question :question:, image :microscope:

#860 - import problems after installing with 'squidpy[interactive]'

Issue - State: closed - Opened by Zaf4 4 months ago - 4 comments

#859 - Sliding window

Pull Request - State: open - Opened by FrancescaDr 4 months ago - 5 comments

#858 - Squidpy unable to read fovs even when they are in the correct format

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

#857 - Release note for 1.6.0

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

#856 - coverage + test

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

#855 - Invalid RGBA argument when use sq.pl.co_occurrence

Issue - State: open - Opened by Donbbit 4 months ago - 1 comment
Labels: plot :hibiscus:

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

Pull Request - State: closed - Opened by pre-commit-ci[bot] 4 months ago

#853 - ImportError: cannot import name 'get_cmap' from 'matplotlib.cm'

Issue - State: closed - Opened by zyll123 4 months ago - 3 comments
Labels: maint :building_construction:

#852 - List Index out of range for loading CellComposites

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

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

Pull Request - State: closed - Opened by pre-commit-ci[bot] 4 months ago

#850 - Image analysis functionality

Issue - State: open - Opened by timtreis 4 months ago
Labels: enhancement :sparkles:, image :microscope:, squidpy2.0

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

Pull Request - State: closed - Opened by pre-commit-ci[bot] 4 months ago

#848 - squidpy.im.ImageContainer cannot process some pyramid tiff (with z > 1)

Issue - State: open - Opened by gdurif 4 months ago - 2 comments
Labels: image :microscope:, sdata compat :milky_way:

#847 - fix precommit and add pre-release test

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

#846 - obsm (spatial, spatial_fov) size seems unreasonably large.

Issue - State: open - Opened by JonatanSahar 5 months ago - 1 comment
Labels: question :question:

#845 - UnidentifiedImageError when reading in Nanostring CosMx Data

Issue - State: open - Opened by keiven-kun 5 months ago - 2 comments
Labels: I/O :cd:

#844 - Documentation of spatial_scatter

Issue - State: open - Opened by schae211 5 months ago - 1 comment
Labels: doc, maint :building_construction:

#843 - Is squidpy.read.visium compatible with Visium HD data?

Issue - State: closed - Opened by sunyumail93 5 months ago - 1 comment

#842 - compute graph base on spatialdata regions and add mask graph based on polygon

Pull Request - State: closed - Opened by giovp 5 months ago - 2 comments

#841 - Analyze Visium H&E data with h5ad

Issue - State: closed - Opened by asmlgkj 5 months ago - 5 comments
Labels: question :question:

#840 - After removing rows with only NaN interactions, none remain.

Issue - State: open - Opened by asmlgkj 5 months ago - 6 comments
Labels: graph :spider_web:

#839 - Failed to open the url with default certificates, trying with certifi. HTTPError: HTTP Error 403: Forbidden

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

#838 - build spatial neighbors graph with spatialdata elements

Issue - State: closed - Opened by giovp 5 months ago
Labels: graph :spider_web:

#837 - `var_by_distance` using polygons annotations

Issue - State: open - Opened by giovp 5 months ago
Labels: enhancement :sparkles:, graph :spider_web:

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

Pull Request - State: closed - Opened by pre-commit-ci[bot] 5 months ago

#835 - Vizgen-MERFISH multiple dataset integration/comparison

Issue - State: open - Opened by HSvitina 5 months ago
Labels: good first issue, question :question:

#834 - neigh_correct when computing spatial graph

Issue - State: open - Opened by wangjiawen2013 6 months ago - 1 comment
Labels: graph :spider_web:

#833 - When attempting to install, dependency "pygeos" gives: module 'configparser' has no attribute 'SafeConfigParser'

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

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

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

#831 - Add function for calculating niches

Pull Request - State: open - Opened by LLehner 6 months ago - 6 comments
Labels: graph :spider_web:, squidpy2.0

#830 - update releases and precommit

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

#829 - Sliding window across spatial neighbourhood

Issue - State: open - Opened by FrancescaDr 6 months ago - 4 comments
Labels: question :question:

#828 - Update template to v0.4.0

Pull Request - State: closed - Opened by scverse-bot 6 months ago

#827 - matplotlib update leads to import error

Issue - State: closed - Opened by LouisK92 6 months ago - 8 comments

#826 - `calculate_image_features()` error with tutorial data

Issue - State: open - Opened by kimsjune 6 months ago - 2 comments
Labels: image :microscope:

#825 - Stacking XYZ dimension images of mouse brain into 3D Volume

Issue - State: open - Opened by sleepingcat4 6 months ago
Labels: image :microscope:, 3d :ice_cube:

#824 - sort_order for pl.spatial_scatter

Issue - State: open - Opened by JBreunig 7 months ago - 1 comment
Labels: plot :hibiscus:

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

Pull Request - State: closed - Opened by pre-commit-ci[bot] 7 months ago

#822 - Clustering according to image features

Issue - State: open - Opened by gboscagli 7 months ago
Labels: graph :spider_web:

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

Pull Request - State: closed - Opened by pre-commit-ci[bot] 7 months ago

#820 - Extracted cropped spot images

Issue - State: closed - Opened by KSimi7 7 months ago - 2 comments

#819 - sq.gr.ligrec crashing kernel/script with VisiumHD (>100k spots/spatial barcodes) - Squidpy incompatible with single-cell level spatial technologies?

Issue - State: closed - Opened by Rafael-Silva-Oliveira 7 months ago - 4 comments
Labels: graph :spider_web:, diff analysis :bar_chart:, speed up :runner:

GitHub / scverse/squidpy issues and pull requests