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Cell phenotype identification

BK Boyd Kenkhuis
AS Antonios Somarakis
LH Lorraine de Haan
OD Oleh Dzyubachyk
MI Marieke E. IJsselsteijn
NM Noel F. C. C. de Miranda
BL Boudewijn P. F. Lelieveldt
JD Jouke Dijkstra
WR Willeke M. C. van Roon-Mom
TH Thomas Höllt
LW Louise van der Weerd
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Superimposing the segmentation masks onto the component image of all membrane markers, four mean intensity values were extracted for each cell. Afterwards, intensity values were normalized imposing Z-score transformation. For the definition of the different microglia cell types Phenograph [25], an unsupervised clustering method, was utilized. For Phenograph 100 nearest neighbours along with the default parameters were selected, in order to avoid overclustering due to the limited amount of markers. Subsequently, for each Phenograph identified cluster the variability of the single-cell marker expression values was examined (Additional file 1: Fig. S3) through a violin plot [26] indicating the variation in each cluster, in parallel with their expression patterns as illustrated in the composite images.

Copyright and License information: The Author(s) ©2021
Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

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