Alternatives and similar repositories for readimc

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

• plevritis-lab / CELESTA
  Automate unsupervised machine learning cell type identification using both protein expressions and cell spatial neighborhood information …
  ☆38Updated last year
• quentinblampey / spatialdata_xenium_explorer
  Interoperability between SpatialData and the Xenium Explorer
  ☆25Updated last year
• JEFworks-Lab / STalign
  Python tool for alignment of spatial transcriptomics (ST) data using diffeomorphic metric mapping
  ☆91Updated last year
• labsyspharm / scimap
  Spatial Single-Cell Analysis Toolkit
  ☆104Updated 5 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…
  ☆16Updated 4 years ago
• ElementoLab / utag
  ☆39Updated last year
• saeyslab / harpy
  Single-cell spatial proteomics analysis that makes you happy!
  ☆48Updated this week
• Vizgen / vizgen-postprocessing
  The Vizgen Post-processing Tool (VPT) enables users to reprocess and refine the single-cell results of MERSCOPE experiments.
  ☆35Updated last year
• CellProfiling / pipex
  A pipeline to transform images into valuable analysis items
  ☆16Updated 5 months ago
• BodenmillerGroup / steinbock
  A toolkit for processing multiplexed tissue images
  ☆67Updated this week
• SchapiroLabor / histoCAT
  Histology Topography Cytometry Analysis Toolbox
  ☆69Updated last month
• linnarsson-lab / FISHscale
  Spatial analysis of FISH data
  ☆34Updated 6 months ago
• nf-core / spatialxe
  ☆24Updated 2 weeks ago
• ciccalab / SIMPLI
  SIMPLI is a highly configurable pipeline for the analysis of multiplexed imaging data.
  ☆39Updated 2 months ago
• YeoLab / bento-tools
  A Python toolkit for subcellular analysis of spatial transcriptomics data
  ☆84Updated 3 weeks ago
• scverse / spatialdata-io
  ☆82Updated this week
• SydneyBioX / BIDCell
  Biologically-informed deep learning for cell segmentation of subcelluar spatial transcriptomics data
  ☆46Updated last year
• theislab / spapros
  Python package for Probe set selection for targeted spatial transcriptomics.
  ☆47Updated 3 weeks ago
• seqscope / ficture
  ☆41Updated last month
• raphael-group / paste2
  Probabilistic Alignment of Spatial Transcriptomics Experiments v.2
  ☆41Updated 9 months ago
• fish-quant / ComSeg
  comseg
  ☆24Updated 10 months ago
• BodenmillerGroup / cytomapper
  R package for visualization of highly multiplexed imaging data
  ☆34Updated 6 months ago
• yuqiyuqitan / SPACEc
  ☆51Updated 5 months ago
• BodenmillerGroup / IMCDataAnalysis
  R based workflow for multiplexed imaging data
  ☆36Updated 4 months ago
• saeyslab / napari-sparrow
  https://sparrow-pipeline.readthedocs.io/en/latest/
  ☆33Updated last week
• ZhuangLab / MERFISH_analysis
  Matlab software for the analysis of MERFISH data and the construction of MERFISH probes.
  ☆50Updated 4 years ago
• 10XGenomics / janesick_nature_comms_2023_companion
  Code companion to the publication "High resolution mapping of the breast cancer tumor microenvironment using integrated single cell, spat…
  ☆28Updated 2 years ago
• wollmanlab / JSTA
  ☆15Updated 3 years ago
• raphael-group / STARCH
  Spatial Transcriptomics Algorithm Reconstructing Copy-number Heterogeneity
  ☆28Updated last year
• wanglab-broad / ClusterMap
  ClusterMap for multi-scale clustering analysis of spatial gene expression
  ☆46Updated 5 months ago