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2023-Birrer et al-Cytometry A

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mleipold

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Post Fri Jan 06, 2023 4:54 pm

2023-Birrer et al-Cytometry A

"OMIP-088: Twenty-target imaging mass cytometry panel for major cell populations in mouse formalin fixed paraffin embedded liver"
Fabienne Birrer, Tess Brodie, Deborah Stroka
Cytometry A. 2023
https://doi.org/10.1002/cyto.a.24714

- "DATA AVAILABILITY STATEMENT All raw data (TXT files), output from steinbock DeepCell cell segmentation, and R scripts required to reproduce Figure 1 will be placed in Zenodo (open research repository) upon publication."
- no Zenodo link in MiFlowCyt checklist either
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mleipold

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Joined: Fri Nov 01, 2013 5:30 pm

Location: Stanford HIMC, CA, USA

Post Mon Mar 13, 2023 4:43 pm

Re: 2023-Birrer et al-Cytometry A

"DATA AVAILABILITY STATEMENT

All raw data (TXT files), output from steinbock DeepCell cell segmentation, and R scripts required to reproduce Figure 1 are in zenodo at the following link: https://zenodo.org/record/7516398#.Y72AFBXMIaF "
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sgranjeaud

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Location: Marseille, France

Post Mon Mar 13, 2023 5:23 pm

Re: 2023-Birrer et al-Cytometry A

The Zenodo repository contains 4 TIFF images in the img folder. The 4 TEXT files in the raw folder are text tabulated files. The "210928_all tissues full panel_Liver 1 Day 2_13.txt" file contains the following columns (leading space characters are in the file).

Start_push
End_push
Pushes_duration
X
Y
Z
Background(ArAr80Di)
Background(I127Di)
Background(Xe131Di)
Background(Xe134Di)
Background(Ba138Di)
a-SMA(Pr141Di)
CD19(Nd142Di)
Nd143(Nd143Di)
Nd144(Nd144Di)
Nd145(Nd145Di)
HNF(Nd146Di)
Sm147(Sm147Di)
Nd148(Nd148Di)
CD11b(Sm149Di)
Nd150(Nd150Di)
Eu151(Eu151Di)
F4/80(Sm152Di)
CD44(Eu153Di)
CD3e(Sm154Di)
CD317(Gd155Di)
Gd156(Gd156Di)
E-cadherin(Gd158Di)
Ly6-G(Tb159Di)
CD206(Gd160Di)
Dy161(Dy161Di)
Dy162(Dy162Di)
CD161(Dy163Di)
Arginase-1(Dy164Di)
CD4(Ho165Di)
CD74(Er166Di)
CD8a(Er167Di)
Ki-67(Er168Di)
CD31(Tm169Di)
Er170(Er170Di)
Yb171(Yb171Di)
Yb172(Yb172Di)
Yb173(Yb173Di)
Yb174(Yb174Di)
Pan-actin(Lu175Di)
Histon H3(Yb176Di)
BCKG190(BCKG190Di)
DNA1(Ir191Di)
DNA2(Ir193Di)
Background(Pb208Di)

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