CropReader plugin, for auto cropping out from image over 2Gpx
I wrote a new plugin.
I wanted to analyse The Cancer Genome Atlas Digital slides obtained from
GDC, Genomic Data Commons portal’s legacy-archive.
The format of the digital slides is svs, a format for aperio image viewer.
Bioformats can handle with svs but many image files 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 a plugin, CropReader, for auto cropping out tissue object from
large image file and saving as vanilla ImageJ can handle with.
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.