Alternatives and similar repositories for readimc

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

• JEFworks-Lab / STalign
  Python tool for alignment of spatial transcriptomics (ST) data using diffeomorphic metric mapping
  ☆89Updated last year
• plevritis-lab / CELESTA
  Automate unsupervised machine learning cell type identification using both protein expressions and cell spatial neighborhood information …
  ☆37Updated last year
• labsyspharm / scimap
  Spatial Single-Cell Analysis Toolkit
  ☆99Updated 3 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
• BodenmillerGroup / steinbock
  A toolkit for processing multiplexed tissue images
  ☆65Updated last week
• Vizgen / vizgen-postprocessing
  The Vizgen Post-processing Tool (VPT) enables users to reprocess and refine the single-cell results of MERSCOPE experiments.
  ☆33Updated last year
• theislab / spapros
  Python package for Probe set selection for targeted spatial transcriptomics.
  ☆44Updated 3 weeks ago
• quentinblampey / spatialdata_xenium_explorer
  Interoperability between SpatialData and the Xenium Explorer
  ☆24Updated last year
• saeyslab / harpy
  Single-cell spatial proteomics analysis that makes you happy!
  ☆41Updated last week
• SchapiroLabor / histoCAT
  Histology Topography Cytometry Analysis Toolbox
  ☆67Updated last week
• ElementoLab / utag
  ☆39Updated last year
• CellProfiling / pipex
  A pipeline to transform images into valuable analysis items
  ☆15Updated 4 months ago
• linnarsson-lab / FISHscale
  Spatial analysis of FISH data
  ☆32Updated 5 months ago
• ciccalab / SIMPLI
  SIMPLI is a highly configurable pipeline for the analysis of multiplexed imaging data.
  ☆38Updated last month
• YeoLab / bento-tools
  A Python toolkit for subcellular analysis of spatial transcriptomics data
  ☆84Updated 3 months ago
• fish-quant / ComSeg
  comseg
  ☆24Updated 8 months ago
• SydneyBioX / BIDCell
  Biologically-informed deep learning for cell segmentation of subcelluar spatial transcriptomics data
  ☆45Updated last year
• scverse / spatialdata-io
  ☆73Updated last week
• nf-core / spatialxe
  ☆22Updated this week
• seqscope / ficture
  ☆38Updated 2 months ago
• nolanlab / CODEX
  Image processing software for CODEX: driftcompensation, deconvolution, uploading and segmentation
  ☆49Updated 3 years ago
• raphael-group / paste2
  Probabilistic Alignment of Spatial Transcriptomics Experiments v.2
  ☆39Updated 7 months ago
• shuxiaoc / maxfuse
  ☆56Updated last year
• ZhuangLab / MERFISH_analysis
  Matlab software for the analysis of MERFISH data and the construction of MERFISH probes.
  ☆50Updated 4 years ago
• dpeerlab / ENVI
  ☆50Updated 2 weeks ago
• saeyslab / napari-sparrow
  https://sparrow-pipeline.readthedocs.io/en/latest/
  ☆31Updated this week
• acycliq / pciSeq
  A probabilistic cell typing algorithm for spatial transcriptomics.
  ☆25Updated this week
• nolanlab / NeighborhoodCoordination
  Code accompanying our manuscript "Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive f…
  ☆67Updated 11 months ago
• estellad / SpatialExperimentIO
  Read in Xenium, CosMx, Vizgen, STARmap PLUS, seqFISH data as Spatial or SingleCell Experiment object.
  ☆16Updated last month
• angelolab / ark-analysis
  Integrated pipeline for multiplexed image analysis
  ☆97Updated 6 months ago