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Add analysis notebook using MCMICRO #69

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Add analysis notebook using MCMICRO #69

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37 changes: 37 additions & 0 deletions notebooks/analysis/MCMICRO-example-IDC/OME-TIFF/markers.csv
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Original file line number Diff line number Diff line change
@@ -0,0 +1,37 @@
channel_number,cycle_number,marker_name,Filter,excitation_wavelength,emission_wavelength,background,exposure,remove
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Information about those markers is contained in the DICOM file. Doesn't BioFormats DICOM reader extract those into any user-accessible location? If this file needs to be created by the user somehow, this notebook is not generalizable.

0,1,DNA,0,395,431,,,
1,1,Control-488nm,1,488,525,,,
2,1,Control-555nm,2,555,568,,,
3,1,Control-647nm,3,647,671,,,
4,2,DNA 2,4,395,431,,,
5,2,CD31,5,488,525,,,
6,2,Na/K ATPase,6,555,568,,,
7,2,CD45RO,7,647,671,,,
8,3,DNA 3,8,395,431,,,
9,3,Antigen Ki67,9,488,525,,,
10,3,Pan-cytokeratin,10,555,568,,,
11,3,Aortic smooth muscle actin,11,647,671,,,
12,4,DNA 4,12,395,431,,,
13,4,CD4,13,488,525,,,
14,4,14,14,555,568,,,
15,4,15,15,647,671,,,
16,5,DNA5,16,395,431,,,
17,5,CD20,17,488,525,,,
18,5,CD68,18,555,568,,,
19,5,CD8a,19,647,671,,,
20,6,DNA 6,20,395,431,,,
21,6,CD163,21,488,525,,,
22,6,FOXP3,22,555,568,,,
23,6,23,23,647,671,,,
24,7,DNA 7,24,395,431,,,
25,7,25,25,488,525,,,
26,7,Vimentin,26,555,568,,,
27,7,CDX-2,27,647,671,,,
28,8,DNA 8,28,395,431,,,
29,8,Lamin-A/B/C,29,488,525,,,
30,8,Desmin,30,555,568,,,
31,8,CD31,31,647,671,,,
32,9,DNA 9,32,395,431,,,
33,9,PCNA,33,488,525,,,
34,9,Antigen Ki67 2,34,555,568,,,
35,9,Collagen,35,647,671,,,
5 changes: 5 additions & 0 deletions notebooks/analysis/MCMICRO-example-IDC/OME-TIFF/params.yml
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workflow:
start-at: segmentation
stop-at: quantification
segmentation: ilastik
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Can you add something in the notebook text (in the beginning) that would explain what this workflow is actually doing, how to access documentation, how to find alternative workflows? There is a reference to https://mcmicro.org/parameters/other.html#ilastik, but it is deep in the notebook, and even then it does not say what analysis this actual workflow is doing.

segmentation-channel: 1
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