Alternatives and similar repositories for vizgen-postprocessing

Users that are interested in vizgen-postprocessing are comparing it to the libraries listed below

• JEFworks-Lab / STalign
  Python tool for alignment of spatial transcriptomics (ST) data using diffeomorphic metric mapping
  ☆91Updated last year
• linnarsson-lab / FISHscale
  Spatial analysis of FISH data
  ☆34Updated 6 months ago
• scverse / spatialdata-io
  ☆80Updated last week
• labsyspharm / scimap
  Spatial Single-Cell Analysis Toolkit
  ☆104Updated 5 months ago
• plevritis-lab / CELESTA
  Automate unsupervised machine learning cell type identification using both protein expressions and cell spatial neighborhood information …
  ☆38Updated last year
• saeyslab / harpy
  Single-cell spatial proteomics analysis that makes you happy!
  ☆45Updated last week
• ZhuangLab / MERFISH_analysis
  Matlab software for the analysis of MERFISH data and the construction of MERFISH probes.
  ☆50Updated 4 years ago
• wanglab-broad / ClusterMap
  ClusterMap for multi-scale clustering analysis of spatial gene expression
  ☆46Updated 5 months ago
• wollmanlab / JSTA
  ☆15Updated 3 years ago
• HiDiHlabs / ssam
  ☆27Updated last year
• YeoLab / bento-tools
  A Python toolkit for subcellular analysis of spatial transcriptomics data
  ☆84Updated 2 weeks ago
• quentinblampey / spatialdata_xenium_explorer
  Interoperability between SpatialData and the Xenium Explorer
  ☆25Updated last year
• saeyslab / napari-sparrow
  https://sparrow-pipeline.readthedocs.io/en/latest/
  ☆33Updated last week
• fish-quant / ComSeg
  comseg
  ☆24Updated 9 months ago
• scverse / napari-spatialdata
  Interactive visualization of spatial omics data
  ☆73Updated last week
• theislab / spapros
  Python package for Probe set selection for targeted spatial transcriptomics.
  ☆47Updated 3 weeks ago
• seqscope / ficture
  ☆41Updated last month
• emanuega / MERlin
  MERlin is an extensible analysis pipeline applied to decoding MERFISH data
  ☆35Updated 4 years ago
• acycliq / pciSeq
  A probabilistic cell typing algorithm for spatial transcriptomics.
  ☆25Updated 3 weeks ago
• EliHei2 / segger_dev
  a cutting-edge cell segmentation model specifically designed for single-molecule resolved spatial omics datasets. It addresses the challe…
  ☆80Updated 3 weeks ago
• raphael-group / paste2
  Probabilistic Alignment of Spatial Transcriptomics Experiments v.2
  ☆41Updated 9 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 / readimc
  Python package for reading imaging mass cytometry (IMC) files
  ☆17Updated last week
• camlab-bioml / starling
  Segmentation error aware clustering for multiplexed imaging
  ☆19Updated 10 months ago
• camlab-bioml / astir
  astir | Automated cell identity from single-cell multiplexed imaging and proteomics 🖥🔬✨
  ☆57Updated 5 months ago
• nf-core / spatialxe
  ☆24Updated 2 weeks ago
• SydneyBioX / BIDCell
  Biologically-informed deep learning for cell segmentation of subcelluar spatial transcriptomics data
  ☆46Updated last year
• CellProfiling / pipex
  A pipeline to transform images into valuable analysis items
  ☆16Updated 5 months ago
• haniffalab / webatlas-pipeline
  A data pipeline built in Nextflow to process spatial and single-cell experiment data for visualisation in WebAtlas
  ☆65Updated 5 months ago
• hubmapconsortium / spatial-transcriptomics-pipeline
  ☆29Updated last year