Alternatives and similar repositories for cytominer

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

• broadinstitute / cell-health
  Predicting Cell Health with Morphological Profiles
  ☆37Updated 3 years ago
• camlab-bioml / astir
  astir | Automated cell identity from single-cell multiplexed imaging and proteomics 🖥🔬✨
  ☆53Updated last year
• dpeerlab / PhenoGraph
  Subpopulation detection in high-dimensional single-cell data
  ☆69Updated 4 years ago
• eiriniar / CellCnn
  Representation Learning for detection of phenotype-associated cell subsets
  ☆65Updated 4 years ago
• ciccalab / SIMPLI
  SIMPLI is a highly configurable pipeline for the analysis of multiplexed imaging data.
  ☆37Updated last year
• CellProfiler / CellProfiler-plugins
  Community-contributed and experimental CellProfiler modules.
  ☆66Updated last week
• nolanlab / CODEX
  Image processing software for CODEX: driftcompensation, deconvolution, uploading and segmentation
  ☆47Updated 3 years ago
• SchapiroLabor / histoCAT
  Histology Topography Cytometry Analysis Toolbox
  ☆67Updated last year
• DistributedScience / Distributed-CellProfiler
  Run encapsulated docker containers with CellProfiler in the Amazon Web Services infrastructure.
  ☆41Updated 2 weeks ago
• carpenterlab / 2016_Bray_NatureProtocols
  Supporting data files, documentation, and updated tips for the Cell Painting protocol
  ☆21Updated 3 years ago
• BodenmillerGroup / ImcSegmentationPipeline
  A pixel classification based multiplexed image segmentation pipeline
  ☆96Updated last year
• nf-core / imcyto
  Image Mass Cytometry analysis pipeline
  ☆25Updated 3 weeks ago
• cytomining / copairs
  Find profile pairs and compute metrics between them.
  ☆17Updated 3 weeks ago
• HiDiHlabs / ssam
  ☆27Updated 8 months ago
• burtonrj / CytoPy
  A data-centric flow/mass cytometry automated analysis framework
  ☆41Updated 5 months ago
• nolanlab / vortex
  VorteX Clustering Environment - Java graphical tool for single-cell analysis, clustering and visualization. Latest release:
  ☆34Updated 2 years ago
• labsyspharm / scimap
  Spatial Single-Cell Analysis Toolkit
  ☆92Updated last month
• jacoblevine / PhenoGraph
  Subpopulation detection in high-dimensional single-cell data
  ☆138Updated 4 years ago
• SofieVG / FlowSOM
  Using self-organizing maps for visualization and interpretation of cytometry data
  ☆64Updated last year
• PreibischLab / STIM
  Library for managing, storage, viewing, and working with spatial transcriptomics data using Imglib2, N5, BigDataViewer and Fiji.
  ☆27Updated 3 weeks ago
• Mr-Milk / SpatialTis
  Spatial analysis toolkit for single cell multiplexed tissue data
  ☆30Updated 9 months ago
• broadinstitute / deepometry
  Image classification for imaging flow cytometry.
  ☆29Updated 5 months ago
• Hatchin / FlowSOM
  FlowSOM algorithm in Python, using self-organizing maps and minimum spanning tree for visualization and interpretation of cytometry data
  ☆33Updated 3 years ago
• labsyspharm / mcmicro
  Multiple-choice microscopy pipeline
  ☆132Updated 3 months ago
• cytomining / DeepProfiler
  Morphological profiling using deep learning
  ☆118Updated 8 months ago
• carpenter-singh-lab / 2023_Cimini_NatureProtocols
  Optimizing the Cell Painting assay for image-based profiling
  ☆20Updated 5 months ago
• TaylorResearchLab / scedar
  Single-cell exploratory data analysis for RNA-Seq
  ☆40Updated 4 years ago
• carpenter-singh-lab / 2022_Haghighi_NatureMethods
  High-Dimensional Gene Expression and Morphology Profiles of Cells across 28,000 Genetic and Chemical Perturbations
  ☆48Updated 5 months ago
• BIMSBbioinfo / maui
  Multi-omics Autoencoder Integration: Deep learning-based heterogenous data analysis toolkit
  ☆49Updated last year
• MannLabs / scPortrait
  scPortrait is a scalable toolkit to generate single-cell representations from raw microscopy images
  ☆47Updated this week