May 12, 2020
Version 2
Imaging Mass Cytometry Modality Overview V.2
- 1Unversity of Zurich;
- 2University of Florida
- Human BioMolecular Atlas Program (HuBMAP) Method Development CommunityTech. support email: Jeff.spraggins@vanderbilt.edu
Protocol Citation: Michelle Daniel, Marda Jorgensen 2020. Imaging Mass Cytometry Modality Overview . protocols.io https://dx.doi.org/10.17504/protocols.io.bgatjsen
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: May 12, 2020
Last Modified: October 02, 2020
Protocol Integer ID: 36915
Keywords: HuBMAP, Imaging Mass Cytometry, TMC-Florida/Zurich
Process donor organs into samples for analysis.
Register organ donor, organs received, and common coordinate region information in the HuBMAP UUID generator at
Prepare paraffin blocks from tissue samples.
Cassette Processing: dx.doi.org/10.17504/protocols.io.8nzhvf6
Paraffin Embedding: dx.doi.org/10.17504/protocols.io.bam9ic96
Package and send paraffin blocks to the Bodenmiller lab: dx.doi.org/10.17504/protocols.io.bf5njq5e
Conjugate primary antibodies using the Maxpar Antibody Labeling Kit: dx.doi.org/10.17504/protocols.io.bf5jjq4n
Cut and mount paraffin sections for staining and analysis.
Sectioning: dx.doi.org/10.17504/protocols.io.bfz4jp8w
Antibody staining of paraffin sections for Imaging Mass Cytometry: dx.doi.org/10.17504/protocols.io.bfz8jp9w
Prepare a slide to use for compensation: dx.doi.org/10.17504/protocols.io.bf2djqa6
Tune the Image Mass Cytometer for acquisition: dx.doi.org/10.17504/protocols.io.bf2gjqbw
Data Acquisition by Image Mass Cytometry: dx.doi.org/10.17504/protocols.io.bf2ijqce
Compensation Slide Acquistion: dx.doi.org/10.17504/protocols.io.bf2jjqcn
Image Processing and Segmentation: https://github.com/BodenmillerGroup/ImcSegmentationPipeline
Load Imaging Mass Cytometry Datasets onto Hipergator:
IMC_Transfer Data Zurich to HPG.docx Prepare and upload data to the HuBMAP HIVE Globus landing pad using Hipergator.
IMC Transfer data from Hipergator to HuBMAP HIVE Globus.docx