Open Microscopy Environment

Hi all,

We often have very large images to open, and while cropping certainly helps, I was wondering if it were at all possible to add an option to the cropper for the step, like there is for the slices, channels and time points?

It would be great if I could open the whole image, but read only one pixel out of 50 in XY so that I have a sampled version of my image, which would help me define a crop area which I can then apply to the full size image.

Best

Oli

Hi Oli,

Cross-linking this question to the related Fiji thread for completeness.

For large images, the canonical way to achieve the workflow what you describing is usually to access images of lower resolution, define a region of interest and convert this region into the coordinates of the full resolution image. For typical pyramidal formats like Aperio SVS or Hamamatsu NDPI, subsampled images are pre-computed, stored into the file format and accessible through the Bio-Formats subresolution API. For large images with no pyramidal levels, there is no immediate API in Bio-Formats allowing to retrieve a subsamples version of the image.

Best,
Sebastien