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PathologyDataScience / HistomicsML2

A tool for training machine-learning models with whole-slide imaging datasets
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TIFF conversion #70

Closed slee172 closed 3 years ago

slee172 commented 3 years ago

@Reasat Thanks for the suggestions! I think excluding the whitespaces while converting to tiff seems logical. There is a function in vips im_extract_areabands which allows extraction of a rectangular portion. https://linux.die.net/man/3/im_extract_bands I think I can pass on the ROI and convert the are to tiff

But I need to understand the parameters going into the below line in create_tiff.sh file.

`vips im_extract_bands --vips-cache-trace --vips-progress $tile $outfilepath.svs.dzi.tif:jpeg:99,tile:256x256,pyramid,,,,8 0 3

'jpeg:99,tile:256x256,pyramid,,,,8 0 3' , I understand that the image is going through a jpg compression before saving but what is the significance of the other parameters? i.e., 256, pyramid, the bunch of commas, 8, 0 and 3 etc.

slee172 commented 3 years ago

@Reasat For the command information, refer to here https://iipimage.sourceforge.io/documentation/images/