DATA ANALYSIS TOOLS

Single Cell Analysis

Spatial

Bioconductor CyTOF workflow (Malgorzata Nowicka):

Publication

Package

Steinbock – a single-cell spatial analysis tool:

Differential discovery in high-dimensional cytometry via high-resolution clustering (DiffCyt;  Lukas M Weber):

DiffCyt

SpaceCat allows you to easily generate hundreds of distinct features from multiplexed imaging data to enable easy downstream quantification.

SpaceCat: Generate a Spatial Catalogue from multiplexed imaging experiments

Cytometry dATa anALYSis Tools (CATALYST; Helena L Crowell, Mark D Robinson, Vito RT Zanotelli, Stéphane Chevrier, and Bernd Bodenmiller):

CATALYST

PANEL DESIGN

Standard Biotools offers a panel designer.
Paneldesigner

ANTIBODY SOURCES

Here a short selection of antibodies from companies we used as source for unlabeled – mass cytometry ready antibodies:

Metal-labeled antibodies and kits – ready to use:

WEBINARS

Society for Immunotherapy of Cancer (SITC) Computational Immuno-oncology Webinar Series:

PROTOCOLS

JoVE paper showing how to stain tissue for mass cytometry:

Tissue Immunostaining for Imaging Mass Cytometry. (2024). JoVE. JoVE Encyclopedia of Experiments: Biological Techniques. 

Protocol for labeling antibodies for mass cytometry from the HuBMAP consortium:

Antibody labeling using the MAXPAR antibody labeling kit.