> Links to: Protocols, User-Guides, Tips/Tricks/WebTool Links > Links to: Data Analysis Software and Toolkits: For SMC and For IMC > Links to: Selected Vendors/Distributors, AU Core Facilities, CyTOF User Groups
Protocols, User-Guides:
Standard BioTools (formally Fluidigm) Protocols and User Guides
Selected Published IMC Protocols (Imaging mass cytometry)
Imaging Mass Cytometry in Immuno-Oncology: Overview of the IMC workflow from sample fixation (FFPE) to analysis, with a focus on multiplex panel design and tissue staining.
FCS Express Template for 10-Tube Tritration (Link)
Cell Cryopreservation/freezing after Staining
Fluidigm AppNote: Impact of Cryopreservation on Performance of the Maxpar Direct Immune Profiling System (Link)
WebTools
CyTOF Template Creator Type: Free Shiny app for creating a Panel Template for use in CyTOF. (Tested with CyTOF software v. 6.7.1014 and 7.0.8493).
CyTOF Panel Designer (Type: Free; needs registration and password creation at DVSsciences.com) Panel Designer v2.0 is available to explore and create new panels with professional advice from their local Field Applications Specialists (from Standard BioTools)
Data Analysis Software and Toolkits
For SMC:
Commercial SMC Data Analysis Software:
FlowJo (R-Plugins) Type: Commercial, used at MCU Offline Platform for single-cell flow suspension cytometry analysis
FCS Express Template for 10-Tube Tritration (Link)
OmiQ Type: Commercial, not available at MCU Online Platform for single-cell suspension cytometry analysis
Cytobank Type: Commercial, not available at MCU Online Platform for single-cell suspension cytometry analysis
CellEngine Type: Commercial, not available at MCU Online Platform for single-cell suspension cytometry analysis
Free SMC Data Analysis Software/Scripts/Pipelines:
Cyclospore Offline Tool for the analysis of mass cytometry (CyTOF) data
Vortex VorteX Clustering Environment - Java graphical tool for single-cell analysis, clustering and visualization More info from the ClambeyLab: pdf-Link
Accense Automatic Classification of Cellular Expression by Nonlinear Stochastic Embedding
Catalyst R based tool to provide a pipeline for preprocessing of cytometry data, including i) normalization using bead standards, ii) single-cell deconvolution, and iii) bead-based compensation.
Spectre R package and computational toolkit that enables comprehensive end-to-end integration, exploration, and analysis of high-dimensional cytometry, spatial/imaging, or single-cell data from different batches or experiments
Cyanus "CYtometry ANalysis Using Shiny": Integrated the methods from the CATALYST package for preprocessing, visualization and clustering. For differential abundance detection, we included the diffcyt methods diffcyt-DA-edgeR, diffcyt-DA-voom and diffcyt-DA-GLMM.
CytofKit(2) R based Shiny App: An integrated mass cytometry data analysis pipeline that enables simultaneous illustration of cellular diversity and progression.
Premessa R package for pre-processing of flow and mass cytometry data, that includes panel editing/renaming for FCS files, bead-based normalization and debarcoding.
CyTOFPower R tool to predict the power of CyTOF experiments in the context of differential state analyses. The package provides a shiny app with two options to predict the power of an experiment: i. generation of in-sicilico CyTOF data, using users input ii. browsing in a grid of parameters for which the power was already precomputed.
CyCombine R-package cyCombine allows for robust integration of single-cell cytometry datasets within and across technologies.
CyTOF workflow (2023) Differential discovery in high-throughput high-dimensional cytometry datasets.Workflow offers different analysis paths, including association of cell type abundance with a phenotype or changes in signaling markers within specific subpopulations, or differential analyses of aggregated signals.
CyClone (2023), publication link An accessible pipeline to analyze, evaluate, and optimize multiparametric cytometry data (R-script): "Benchmarked and validated Cyclone on mass cytometry (CyTOF), full-spectrum fluorescence-based cytometry, and multiplexed immunofluorescence (IF)"
PICAFlow (2023), publication link A complete R workflow dedicated to flow/mass cytometry data, from pre-processing to deep and comprehensive analysis.
URSA (2023), publication link An automated multi-omics package for single-cell analysis, Ursa is an R package consisting of seven single-cell omics automated analysis workflows. One-liner command for each omics to run a full post-quantification analysis for the omics. Six single-cell (sc) omics and one bulk omics include: scRNA-sequencing (sc), scATAC-sequencing (sc), scImmune profiling (sc), scCNV (sc), CyTOF (sc), Flow cytometry (sc), Spatial transcriptomics (bulk)
ImmCellTyper: (2023) publication link Cytof data analysis toolkit with cell population auto-annotation function: It has a novel in house semi-supervised clustering tool named BinaryClust, which enables automatic classification and annotation of main cell types as well as in-depth interrogation of certain subpopulation of interest.
For IMC:
Free IMC Data Analysis Software/Scripts/Pipelines:
Free Standalone Software/Tools/Plugins:
MCD viewer Type: Free Post-acquisition data processing software that allows users to visualize, review, and export Imaging Mass Cytometry™ data acquired with the Hyperion™ Imaging System and CyTOF® Software
histoCAT Type: Free Histology Topography Cytometry Analysis Toolbox (histoCAT) is a package to visualize and analyse multiplexed image cytometry data interactively.
ImaCyte Type: Free Interactive tool for data-driven exploration of Imaging Mass Cytometry data
Ilastik Type: Free Interactive learning and segmentation toolkit
Deep Cell Label (Free) DeepCell Label is a data labeling tool to segment images into instance labels, mapping each pixel to an object in the image.
Omero Type: Free Open microscopy enviroment for maniging your images
3D Slicer / TITAN Type:Free TITAN is an extension developed for 3D Slicer that is responsible for the pre-processing and analysis tasks of imaging mass cytometry (IMC) data
Fiji Type: Free Fiji is an image processing package—a “batteries-included” distribution of ImageJ2, bundling a lot of plugins which facilitate scientific image analysis.
Free Tools/Pipelines:
Multiplexed Image Analysis Tools, developed from the Bodenmiller Lab: Link
steinbock for containerized image processing and segmentation.
napari-imc for interactive visualization of IMC raw data in napari.
cytomapper for multiplexed image visualization in R.
cytoviewer for interactive multiplexed image visualization in R.
imcRtools for single-cell and spatial analysis in R.
IMCDataAnalysis for a reproducible workflow on multiplexed image downstream analysis in R.
imcdatasets for a collection of publicly available IMC datasets in R.
Spectre Type: Free (https://immunedynamics.io/spectre/#protocols) R package and computational toolkit that enables comprehensive end-to-end integration, exploration, and analysis of high-dimensional cytometry, spatial/imaging, or single-cell data from different batches or experiments
nfcore/ImCyto Type: Free nfcore/imcyto is a bioinformatics analysis pipeline used for image segmentation and extraction of single cell expression data. The pipeline is built using Nextflow. If you want to use it in a windows enviroment, check here: Deploy a complete Nextflow development environment on Windows 10. (Note: May interfear with your windows admin rights)
RUNIMC Type: Free An R-based package for imaging mass cytometry data analysis and pipeline validation: Publication
Cytomapper Type: Free A computational tool written in R, that enables visualization of pixel- and cell-level information obtained by multiplexed imaging. Publication. In addition, cytomapper includes a Shiny application that allows hierarchical gating of cells based on marker expression and visualization of selected cells in corresponding images.
SIMPLI Type: Free (Linux only?) An agnostic pipeline for the analysis of highly multiplexed histological imaging data. SIMPLI performs all the workflow steps: preprocessing, cell-segmentation, phenotyping, as well as spatial and pixel-level analysis. SIMPLI is available at: https://github.com/ciccalab/SIMPLI ; Publication
"Zaidi"-IMC Pipeline workshop (2022) End-to-End Analysis of Imaging Mass Cytometry Data to Study Heterogeneity in Tumor Microenvironments (Pipeline): featuring: QuPath, IMC-converter, StarDist, Python; YouTube Video Image dataset, QuPath project, and code are all available here.
MCMICRO (Multiple-choice microscopy pipeline) (2022) An end-to-end processing pipeline that transforms multi-channel whole-slide images into single-cell data. Requires: NextFlow, Docker; Windows: Linux Subssytem or Galaxy enviroment
CellX The Danish Single Cell Examination Platform (CellX) is a national research platform/infrastructure dedicated to single cell and spatial omics analysis.