matlab-tag-reader

Version 1.0 (2.16 KB) by Aditya Jain
Take a SliceOMatic .TAG file and read it as a uint16 array in MATLAB.
10 Downloads
Updated 10 Jul 2021

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.

Cite As

Rishab Jain (2021). matlab-tag-reader (https://github.com/RJain12/matlab-tag-reader/releases/tag/1.0), GitHub. Retrieved July 10, 2021.

MATLAB Release Compatibility
Created with R2021a
Compatible with any release
Platform Compatibility
Windows macOS Linux
Acknowledgements

Inspired by: Sliceomatic

Community Treasure Hunt

Find the treasures in MATLAB Central and discover how the community can help you!

Start Hunting!
Version Published Release Notes
1.0

To view or report issues in this GitHub add-on, visit the GitHub Repository.
To view or report issues in this GitHub add-on, visit the GitHub Repository.