Alternatives and similar repositories for MERlin

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

• Vizgen / vizgen-postprocessing
  The Vizgen Post-processing Tool (VPT) enables users to reprocess and refine the single-cell results of MERSCOPE experiments.
  ☆30Updated 11 months ago
• wahlby-lab / graph-iss
  Graph-based Decoding for In Situ Sequencing
  ☆10Updated 5 years ago
• scverse / napari-spatialdata
  Interactive visualization of spatial omics data
  ☆64Updated last week
• hubmapconsortium / spatial-transcriptomics-pipeline
  ☆29Updated last year
• wanglab-broad / ClusterMap
  ClusterMap for multi-scale clustering analysis of spatial gene expression
  ☆46Updated 2 months ago
• ZhuangLab / MERFISH_analysis
  Matlab software for the analysis of MERFISH data and the construction of MERFISH probes.
  ☆50Updated 4 years ago
• scverse / spatialdata-io
  ☆68Updated last week
• acycliq / pciSeq
  A probabilistic cell typing algorithm for spatial transcriptomics.
  ☆24Updated 2 months ago
• JaneliaSciComp / multifish
  EASI-FISH analysis pipeline for spatial transcriptomics
  ☆35Updated 9 months ago
• HiDiHlabs / ssam
  ☆27Updated 10 months ago
• YeoLab / bento-tools
  A Python toolkit for subcellular analysis of spatial transcriptomics data
  ☆82Updated last month
• PreibischLab / RS-FISH
  Tool for precise, interactive, fast and scalable FISH spot detection
  ☆49Updated 6 months ago
• labsyspharm / scimap
  Spatial Single-Cell Analysis Toolkit
  ☆94Updated last month
• linnarsson-lab / FISHscale
  Spatial analysis of FISH data
  ☆31Updated 3 months ago
• MannLabs / scPortrait
  scPortrait is a scalable toolkit to generate single-cell representations from raw microscopy images
  ☆50Updated this week
• multiFISH / EASI-FISH
  Tools and scripts for EASI-FISH image data analysis
  ☆17Updated 2 years ago
• vitessce / vitessce-python
  Python API and Jupyter widget for Vitessce
  ☆53Updated this week
• ciccalab / SIMPLI
  SIMPLI is a highly configurable pipeline for the analysis of multiplexed imaging data.
  ☆38Updated 2 years ago
• PreibischLab / STIM
  Library for managing, storage, viewing, and working with spatial transcriptomics data using Imglib2, N5, BigDataViewer and Fiji.
  ☆29Updated 3 months ago
• JEFworks-Lab / STalign
  Python tool for alignment of spatial transcriptomics (ST) data using diffeomorphic metric mapping
  ☆86Updated last year
• beliveau-lab / PaintSHOP_pipeline
  A scalable machine learning pipeline for probe specificity prediction.
  ☆14Updated last year
• wollmanlab / JSTA
  ☆15Updated 3 years ago
• linnarsson-lab / brainmap
  Allen Brain Atlas utilities, parsers and data structures
  ☆11Updated 8 years ago
• rockdeme / chrysalis
  Powerful and lightweight package to identify tissue compartments in spatial transcriptomics datasets.
  ☆17Updated 2 months ago
• linnarsson-lab / pysmFISH
  Analysis of smFISH data
  ☆11Updated 7 years ago
• BodenmillerGroup / readimc
  Python package for reading imaging mass cytometry (IMC) files
  ☆16Updated this week
• fish-quant / big-fish
  Toolbox for the analysis of smFISH images.
  ☆68Updated last year
• angelolab / ark-analysis
  Integrated pipeline for multiplexed image analysis
  ☆93Updated 4 months ago
• CellProfiling / pipex
  A pipeline to transform images into valuable analysis items
  ☆14Updated 2 months ago
• saeyslab / napari-sparrow
  https://sparrow-pipeline.readthedocs.io/en/latest/
  ☆31Updated this week