I wrote an imageJ plugin.
I wanted to analyse The Cancer Genome Atlas Digital slides obtained from genomic data commons portal’s legacy-archive.
The format of the digital slides is svs, a format for aperio image viewer.
Bioformats can handle svs but many image in TCGA digital slides are over 2G pixel.
So imageJ fails to import such a large image file with “java.lang.illegalArgumentException: Array size too large”.
However, in the slide data, there is large white, background area and tissue objects are almost within 2 G pixel.
And bioformats allows to crop out partial image if within 2G px.
So I wrote plugin for auto cropping out tissue object from large image file and saving as zipped tif.
If anyone encounters same problem, please use this.
Or if this is reinventing the wheel, please tell me.
This is my first java programming. I will appreciate any suggestion.