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.
  ☆27Updated 9 months ago
• ZhuangLab / MERFISH_analysis
  Matlab software for the analysis of MERFISH data and the construction of MERFISH probes.
  ☆50Updated 3 years ago
• hubmapconsortium / spatial-transcriptomics-pipeline
  ☆29Updated last year
• scverse / napari-spatialdata
  Interactive visualization of spatial omics data
  ☆61Updated last week
• wahlby-lab / graph-iss
  Graph-based Decoding for In Situ Sequencing
  ☆10Updated 5 years ago
• YeoLab / bento-tools
  A Python toolkit for subcellular analysis of spatial transcriptomics data
  ☆80Updated 3 weeks ago
• JaneliaSciComp / multifish
  EASI-FISH analysis pipeline for spatial transcriptomics
  ☆35Updated 7 months ago
• scverse / spatialdata-io
  ☆63Updated 2 weeks ago
• linnarsson-lab / FISHscale
  Spatial analysis of FISH data
  ☆30Updated last month
• acycliq / pciSeq
  A probabilistic cell typing algorithm for spatial transcriptomics.
  ☆24Updated 3 weeks ago
• wanglab-broad / ClusterMap
  ClusterMap for multi-scale clustering analysis of spatial gene expression
  ☆45Updated last month
• labsyspharm / scimap
  Spatial Single-Cell Analysis Toolkit
  ☆92Updated 2 weeks ago
• HiDiHlabs / ssam
  ☆27Updated 9 months ago
• PreibischLab / RS-FISH
  Tool for precise, interactive, fast and scalable FISH spot detection
  ☆49Updated 5 months ago
• ciccalab / SIMPLI
  SIMPLI is a highly configurable pipeline for the analysis of multiplexed imaging data.
  ☆38Updated 2 years ago
• JEFworks-Lab / STalign
  Python tool for alignment of spatial transcriptomics (ST) data using diffeomorphic metric mapping
  ☆81Updated last year
• beliveau-lab / PaintSHOP_pipeline
  A scalable machine learning pipeline for probe specificity prediction.
  ☆14Updated last year
• MannLabs / scPortrait
  scPortrait is a scalable toolkit to generate single-cell representations from raw microscopy images
  ☆47Updated this week
• zjniu / Piscis
  An automatic deep learning algorithm for spot detection in fluorescence microscopy images.
  ☆21Updated 2 weeks ago
• plevritis-lab / CELESTA
  Automate unsupervised machine learning cell type identification using both protein expressions and cell spatial neighborhood information …
  ☆35Updated last year
• fish-quant / big-fish
  Toolbox for the analysis of smFISH images.
  ☆68Updated last year
• saeyslab / napari-sparrow
  https://sparrow-pipeline.readthedocs.io/en/latest/
  ☆29Updated last month
• BodenmillerGroup / readimc
  Python package for reading imaging mass cytometry (IMC) files
  ☆15Updated last week
• linnarsson-lab / pysmFISH
  Analysis of smFISH data
  ☆11Updated 6 years ago
• theislab / spapros
  Python package for Probe set selection for targeted spatial transcriptomics.
  ☆38Updated this week
• GuignardLab / napari-sc3D-viewer
  A plugin to visualise 3D spatial single cell omics
  ☆22Updated 3 weeks ago
• ZhuangLab / MERlin
  MERFISH decoding software
  ☆26Updated 2 years ago
• vitessce / vitessce-python
  Python API and Jupyter widget for Vitessce
  ☆49Updated this week
• camlab-bioml / astir
  astir | Automated cell identity from single-cell multiplexed imaging and proteomics 🖥🔬✨
  ☆53Updated 2 weeks ago
• AllenInstitute / cell_type_mapper
  Repository for storing prototype functionality implementations for the BKP
  ☆29Updated last week