Read steinbock metadata from images.csv

[jwindhager]

With steinbock v0.8.0, as requested by @SchulzDan, image metadata is written to images.csv upon preprocessing. As discussed offline, this metadata should be made available to the imcRtools user through the SingleCellExperiment (please discuss with @SchulzDan what information is relevant).

Please note that the existence of an images.csv file is optional (the user may choose to not use steinbock for preprocessing and to instead directly start from TIFF files) and that the filename can be modified by the user. If such a file is present, it can be expected to adhere to the steinbock "image information" file specifications.

Additional columns that are added specifically when preprocessing IMC data (currently undocumented):

• source (the raw mcd/txt file name)
• recovered (True if an mcd acquisition was recovered from the corresponding txt file, otherwise False)
• acquisition_id
• acquisition_description
• acquisition_posx_um
• acquisition_posy_um
• acquisition_width_um
• acquisition_height_um

The test data in https://github.com/BodenmillerGroup/TestData has been updated.

[nilseling]

Hey @jwindhager, is the images.csv file written out by default? I mean in case the user pre-processes images using steinbock.

[jwindhager]

Yes it is, if the user uses Steinbock IMC preprocessing functionality (specifically, steinbock preprocess imc images)

[nilseling]

Aight! What about other multi-channel images? From the docs it looks like it's always written out with the columns you documented

[nilseling]

Done in 6299fec84e4be05e7cd7c67abc654ca6f222acad

[jwindhager]

Aight! What about other multi-channel images? From the docs it looks like it's always written out with the columns you documented

Currently, preprocessing functionality is provided for IMC only