Alternatives and similar repositories for pixie

Users that are interested in pixie are comparing it to the libraries listed below

• sggao / celllens
  CellLENS: Cross-domain information fusion for enhanced cell population delineation in single-cell spatial-omics data
  ☆29Updated 2 months ago
• Feanor007 / MESA
  A python package for Multiomics and Ecological Spatial Analysis (MESA)
  ☆21Updated 5 months ago
• saeyslab / harpy
  Single-cell spatial proteomics analysis that makes you happy!
  ☆38Updated this week
• ElementoLab / utag
  ☆39Updated last year
• quentinblampey / spatialdata_xenium_explorer
  Interoperability between SpatialData and the Xenium Explorer
  ☆24Updated last year
• labsyspharm / scimap
  Spatial Single-Cell Analysis Toolkit
  ☆99Updated 3 months ago
• scverse / spatialdata-notebooks
  ☆59Updated this week
• scverse / spatialdata-io
  ☆72Updated this week
• camlab-bioml / starling
  Segmentation error aware clustering for multiplexed imaging
  ☆18Updated 8 months ago
• klarman-cell-observatory / PowerAnalysisForSpatialOmics
  ☆28Updated last year
• MICS-Lab / novae
  Graph-based foundation model for spatial transcriptomics data. Zero-shot spatial domain inference, batch-effect correction, and many othe…
  ☆54Updated this week
• saeyslab / napari-sparrow
  https://sparrow-pipeline.readthedocs.io/en/latest/
  ☆31Updated last month
• huBioinfo / CytoCommunity
  A spatial omics data analysis tool that enables both unsupervised and supervised discovery of complex tissue cellular neighborhoods from …
  ☆24Updated 5 months ago
• YeoLab / bento-tools
  A Python toolkit for subcellular analysis of spatial transcriptomics data
  ☆83Updated 2 months ago
• chenhcs / SCS
  Sub-cellular spatial transcriptomics Cell Segmentation
  ☆68Updated 2 years ago
• MannLabs / scPortrait
  scPortrait is a scalable toolkit to generate single-cell representations from raw microscopy images
  ☆85Updated last week
• labsyspharm / cylinter
  An Interactive Image Segmentation Filter for Multiplex Microscopy
  ☆31Updated last month
• wanglab-broad / CAST
  CAST package
  ☆40Updated 11 months ago
• sagar87 / spatialproteomics
  Spatialproteomics is a light weight wrapper around xarray with the intention to facilitate the data exploration and analysis of highly mu…
  ☆35Updated last week
• dpeerlab / ENVI
  ☆51Updated 4 months ago
• nolanlab / SpatialScore
  R script for calculating the SpatialScore as described in our manuscript: "Immune cell topography predicts response to PD-1 blockade in c…
  ☆15Updated 4 years ago
• StatBiomed / SpatialDM
  Spatial direct messaging detected by bivariate Moran
  ☆29Updated 2 months ago
• raphael-group / paste2
  Probabilistic Alignment of Spatial Transcriptomics Experiments v.2
  ☆40Updated 7 months ago
• AI4SCR / ATHENA
  ☆35Updated last week
• theislab / spapros
  Python package for Probe set selection for targeted spatial transcriptomics.
  ☆44Updated this week
• SydneyBioX / BIDCell
  Biologically-informed deep learning for cell segmentation of subcelluar spatial transcriptomics data
  ☆45Updated last year
• camlab-bioml / astir
  astir | Automated cell identity from single-cell multiplexed imaging and proteomics 🖥🔬✨
  ☆55Updated 3 months ago
• BiomedicalMachineLearning / stlearn_interactive
  Interactive applications of stlearn
  ☆15Updated 2 years ago
• PMBio / SpatialDE
  Test genes for Spatial Variation
  ☆14Updated 9 months ago
• BodenmillerGroup / steinbock
  A toolkit for processing multiplexed tissue images
  ☆64Updated last week