Open Microscopy Environment

Hi all,

I was wondering how one goes around in IJ macro, Java or Beanshell to open a say 4x downsampled version of a given file (In this case a .czi)

The question being is there a way currently in bioformats to only read one pixel out of 4 in X Y and Z?

Thanks for any info and have a great weekend!

Oli

Hi Oli,

there is no generic way to achieve what you described directly via Bio-Formats i.e. calling openBytes() to return a downsampled X-Y plane. The only exception to this statement is the case of some pyramid file formats where downsampled images are also stored alongside the high-resolution raw data and can be read directly via openBytes().

Otherwise, you might want to direct your question directly to other communities like ImageJ and see if solutions have been implemented.

Best,
Sebastien

Hi Sebastien,

Thank you for the information. I'll go stirr up the imageJ community for further hints, though this leads to a subsidiary question:

The only exception to this statement is the case of some pyramid file formats where downsampled images are also stored alongside the high-resolution raw data and can be read directly via openBytes().

Would the Zeiss CZI format fall within this category?

Best

Oli

Hi Oli,

as far as I can tell, the Zeiss CZI reader does not read multiple levels of resolutions from the Zeiss CZI file format.

We are currently working on a documentation change in order to better expose which file formats store images at multiple resolutions in our supported formats page.

Best,
Sebastien