matlab-tag-reader

Take a SliceOMatic .TAG file and read it as a uint16 array in MATLAB.

There was no existing code to do this online / MATLAB packages available for this purpose.

SliceOmatic 5.0 docs: https://www.tomovision.com/SliceO_Help/index.htm?context=570

Essentially, in this script, we trim out the header by reading the bytes only after a certain point. Then, it's easy because the rest is a 1-dimensional array containing all the data.

Simply resize this array into the shape you need, e.g. 512x512.

This was used this for a segmentation problem, so we read DICOM files into a MATLAB image datastore object:

imds = imageDatastore('my dir would be right here', ...
    'FileExtensions', '.dcm', 'ReadFcn',@(x) dicomread(x));

and pixel datastore (contains the labels/annotations):

pxds = pixelLabelDatastore('folder where tiffs are stored', classNames, labelIDs,'FileExtensions','.tiff');

One thing to look into is instead saving the labels you have (the .TAG)s into a .mat and then use the matReader as a function in your pxds. This would potentially save time and compute resources.

However, since these are simple 2D slices, it was fine saving it as a .tiff in the study.