Rescaling Images In Parallel

groovy
parallel
rescaling
Tags: #<Tag:0x00007fd6a17e71e0> #<Tag:0x00007fd6a17e6e48> #<Tag:0x00007fd6a17e6a60>

#1

Hi all,

Using BioFormats import options, we can define a C Z and T step when importing data, so as to only get a subset.

Unfortunately, there is not a possibility to define an XY step to take just 1 pixel out of 4, for example.

Sometimes this is useful when people want to extract a select part of their data to look at it for example.

The following Groovy script https://gist.github.com/280654785f7a2a79a5093997b50d92bf

Works on multi-series files and saves the XYCZT data to tif (1 tif -> 1 plane) with the selected resizing in XY and Z

It is simple but fast (23s for a 17GB file resampled 2x in XY and 10x in Z). Maybe someone else can have a use for it.

Best

Oli