CropReader plugin, for auto cropping out from image over 2Gpx

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CropReader plugin, for auto cropping out from image over 2Gpx

Keita Fukuyama
 Hi everyone.
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.
https://github.com/fk506cni/ij_plgin

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.

thank you.

fk506cni

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