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Preprint

IMC data

JA James N Arnold
SK Shahram Kordasti

Last updated date: Apr 28, 2022 Views: 628 Forks: 0

original An abbreviated version of this protocol was published in eLife in Apr, 2021
ImmunoCluster provides a computational framework for the nonspecialist to profile high-dimensional cytometry data
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Dear Jonathan,

Many thanks for your message and we are glad that you like our work. As you know, ImmunoCluster uses individual cell expressions to cluster and performs further analysis. BUT the segmentation and generation of single cell data from IMC needs to be done through other packages like this one: https://bodenmillergroup.github.io/ImcSegmentationPipeline/

Then the output can be fed into ImmunoCluster for further analysis as we did in our paper. Obviously for liquid CyTOF or multicolour flowcytometry, we don't need segmentation and data can be analysed directly by ImmunoCluster. I hope these answer your question and happy to answer further questions by email shahram.kordasti@kcl.ac.uk

Best,

Shahram

 

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How to cite：
Readers should cite both the Bio-protocol preprint and the original research article where this protocol was used:
  1. Arnold, J and Kordasti, S(2022). IMC data. Bio-protocol Preprint. bio-protocol.org/prep1647.
  2. Opzoomer, J. W., Timms, J. A., Blighe, K., Mourikis, T. P., Chapuis, N., Bekoe, R., Kareemaghay, S., Nocerino, P., Apollonio, B., Ramsay, A. G., Tavassoli, M., Harrison, C., Ciccarelli, F., Parker, P., Fontenay, M., Barber, P. R., Arnold, J. N. and Kordasti, S.(2021). ImmunoCluster provides a computational framework for the nonspecialist to profile high-dimensional cytometry data. eLife. DOI: 10.7554/eLife.62915

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