Slidescans: p165

This repository constains all the slidescans associated with slide block p165 for the project:

A quantitative analysis of the interplay of environment, neighborhood, and cell state in 3D spheroids

    Vito RT Zanotelli
    Matthias Leutenegger
    Xiao‐Kang Lun
    Fanny Georgi
    Natalie de Souza
    Bernd Bodenmiller

Mol Syst Biol. (2020) 16: e9798
https://doi.org/10.15252/msb.20209798

Please cite this article if you re-use any of the data or code.

Each acquisition follows the naming scheme:

"{operator}_{date}_{slideblock}_{slidescan_flo_number}{suffix}"

e.g. v.zanotelli_20190509_p161_025.czi

With:

•  operator: the slidescan operator
•  date: the acquisition date
•  slideblock: the block cut to produce these slides
•  slidescan_fluo_nr: arbitrary index. Is matched to actual slide number using the metadata file: '20190506_bigstain_selection_final_if_imcalign_v1.csv'
•  suffix:
  •    '.czi': main slidescan
  •    '_pt1.czi': scan of handwritten slide label
  •    '_pt2.csi': coarse slide overview scan

Each 'main slidescan' is usually composed of multiple 'scenes' (regions that were scanned with high resolution). The convention is that each scene corresponds to unique cut that is independently stained. Note that scene numbering is not sequential but rather random.

The slidescans were acquired using an AxioScan.Z1 microscope with:

• Objective: Plan-Apochromat 20x/0.8 M27
• Resolution: nominal 0.325 um/pixel
• Channels:
  • 1) EGFP: Excitation Wavelength: 488 nm, Emission Wavelength: 509 nm
  • 2) DAPI: Excitation Wavelength:  353 nm, Emission Wavelength: 465 nm