Imaging Mass Cytometry workflow for mouse tissues

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Febe
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Joined: Wed Feb 03, 2021 1:53 pm

Imaging Mass Cytometry workflow for mouse tissues

Post by Febe » Wed Feb 03, 2021 2:10 pm

I wanted to share with you our preprint on an optimised Imaging Mass Cytometry pipeline for use on mouse tissue sections.
https://doi.org/10.1101/2021.02.02.429358

In this preprint we describe an antibody panel suitable for mouse tissues, and used Ilastik and CellProfiler to build a sequential segmentation pipeline with cell type specific settings, which can be automated with the use of our nfcore/imcyto pipeline, freely available from: https://github.com/nf-core/imcyto

We think these methods will be very important tools in preclinical studies, as we demonstrate by using it in a lung cancer model, to describe the dramatic remodelling of the tumour microenvironment by a drug targeting the tumour mutation KRAS-G12C.
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