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2022-Tornaas et al-preprint

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mleipold

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Joined: Fri Nov 01, 2013 5:30 pm

Location: Stanford HIMC, CA, USA

Post Mon May 16, 2022 4:58 pm

2022-Tornaas et al-preprint

"Development of an antibody panel for imaging mass cytometry to investigate cancer-associated fibroblast heterogeneity and spatial distribution in archival tissues"
Stian Tornaas, Dimitrios Kleftogiannis, Siren Fromreide, Hilde Ytre-Hauge Smeland, Hans Jørgen Aarstad, Olav Karsten Vintermyr, Lars A. Akslen, Daniela Elena Costea, Harsh Dongre
bioRxiv, posted May 13, 2022
https://doi.org/10.1101/2022.05.12.491175

- will update when/if this is peer-reviewed and published

- "Data Availability Statement

The datasets for this study are publicly available at https://github.com/StiThor/Development- ... fibroblast.
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mleipold

Guru

Posts: 6116

Joined: Fri Nov 01, 2013 5:30 pm

Location: Stanford HIMC, CA, USA

Post Thu May 16, 2024 10:16 pm

Re: 2022-Tornaas et al-preprint

Now published:

Heliyon. 2024
https://doi.org/10.1016/j.heliyon.2024.e31191

Previous Github link doesn't appear to work anymore; " All data to support the conclusions have been either provided. The codes for single cell analysis workflow described here is publicly available at https://github.com/StiThor/IMC_data_analysis.
- This new Github link is predominantly CSV files, not TIFF files (eg, https://github.com/StiThor/IMC_data_ana ... tion_HNSCC)

"Segmentation of raw IMC data was done following the Steinbock framework with Docker container (Deepcell) [19]. Briefly, IMC data was processed by running commands with command prompt (CMD, Windows). A panel.csv file was generated and channels for segmentation (nucleus and cytoplasm/membrane) were chosen. In this study, channels Ir191 and Ir193 were used as nuclear markers, while αSMA, EGFR, CD31, CD4, E-cadherin, CD20 and FSP-1 were used as cytoplasmatic/membrane markers. The end-result was cell masks for each tissue type included in the study. Cell segmentation were quality checked with ImaCytE. For this, mask generated as described above were organized in folders, one for each ROI with image stack ome.tiff files representing all channels from each ROI that were exported from MCD viewer. When segmentation was confirmed with ImaCytE, Steinbock was used to export folder with each individual channel. These folders/images were imported into histoCAT [20] for generation of .csv files that was used for further annotation of single cells into similar clusters in R."

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