Alternatives and similar repositories for pysmFISH

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

• broadchenf / Slideseq
  ☆11Updated 6 years ago
• ZhuangLab / MERFISH_analysis
  Matlab software for the analysis of MERFISH data and the construction of MERFISH probes.
  ☆50Updated 4 years ago
• hubmapconsortium / spatial-transcriptomics-pipeline
  ☆29Updated last year
• linnarsson-lab / FISHscale
  Spatial analysis of FISH data
  ☆31Updated 2 months ago
• theislab / spapros
  Python package for Probe set selection for targeted spatial transcriptomics.
  ☆40Updated 3 weeks ago
• acycliq / pciSeq
  A probabilistic cell typing algorithm for spatial transcriptomics.
  ☆24Updated last month
• BiomedicalMachineLearning / stlearn_interactive
  Interactive applications of stlearn
  ☆15Updated 2 years ago
• linnarsson-lab / brainmap
  Allen Brain Atlas utilities, parsers and data structures
  ☆11Updated 8 years ago
• wanglab-broad / ClusterMap
  ClusterMap for multi-scale clustering analysis of spatial gene expression
  ☆45Updated last month
• Vizgen / vizgen-postprocessing
  The Vizgen Post-processing Tool (VPT) enables users to reprocess and refine the single-cell results of MERSCOPE experiments.
  ☆28Updated 10 months ago
• ciccalab / SIMPLI
  SIMPLI is a highly configurable pipeline for the analysis of multiplexed imaging data.
  ☆38Updated 2 years ago
• beliveau-lab / PaintSHOP_pipeline
  A scalable machine learning pipeline for probe specificity prediction.
  ☆14Updated last year
• emanuega / MERlin
  MERlin is an extensible analysis pipeline applied to decoding MERFISH data
  ☆35Updated 3 years ago
• camlab-bioml / astir
  astir | Automated cell identity from single-cell multiplexed imaging and proteomics 🖥🔬✨
  ☆53Updated last month
• wanglab-broad / mCNS-atlas
  ☆18Updated last year
• AllenInstitute / cell_type_mapper
  Repository for storing prototype functionality implementations for the BKP
  ☆31Updated last week
• saeyslab / napari-sparrow
  https://sparrow-pipeline.readthedocs.io/en/latest/
  ☆29Updated last week
• YeoLab / bento-tools
  A Python toolkit for subcellular analysis of spatial transcriptomics data
  ☆81Updated 2 weeks ago
• ZhuangLab / MERlin
  MERFISH decoding software
  ☆26Updated 2 years ago
• AllenInstitute / scrattch
  Single cell RNA-seq analysis for transcriptomic type characterization
  ☆37Updated this week
• quentinblampey / spatialdata_xenium_explorer
  Interoperability between SpatialData and the Xenium Explorer
  ☆24Updated last year
• niaid / imaris_extensions
  Algorithmic and Utility Extensions for the Imaris Program
  ☆18Updated 10 months ago
• TencentAILabHealthcare / pysodb
  ☆24Updated last year
• nolanlab / SpatialScore
  R script for calculating the SpatialScore as described in our manuscript: "Immune cell topography predicts response to PD-1 blockade in c…
  ☆15Updated 3 years ago
• AhsenChaudhry / Mitochondria-Analyzer
  Mitochondria Analyzer
  ☆22Updated 2 years ago
• fmi-basel / glib-nature2018-materials
  Image Processing Package for the Paper "Self-organization and symmetry breaking in intestinal organoid development"
  ☆11Updated 4 years ago
• JEFworks-Lab / STalign
  Python tool for alignment of spatial transcriptomics (ST) data using diffeomorphic metric mapping
  ☆85Updated last year
• SchapiroLabor / histoCAT
  Histology Topography Cytometry Analysis Toolbox
  ☆67Updated last year
• nf-core / spatialxe
  ☆19Updated last month
• haniffalab / webatlas-pipeline
  A data pipeline built in Nextflow to process spatial and single-cell experiment data for visualisation in WebAtlas
  ☆64Updated last month