Writing Multichannel large tif image into pyramidal OME-tiff

I initially had several channels of a fluorescent image (13 channels) that I then assembled into 1 multipage tiff using the bigtiff writer in MATLAB (since it is 17000 pixel x 34000 pixel x 13 channels). However, because I would like to open it in Qupath, I need a pyramidal version, which would be offered by an OME-TIFF format. Is there a way I can read in my multichannel tiff image and save a pyramidal version that can then be opened in Qupath? Or any other alternative?

[Éric Martineau]

Hi,

Did you find an answer in the end? I want to do something similar and I can't find a solution. I want to perform a z projection of large, multi-channel, multi-plane images and send them in a format I can open with quPath.

Thanks.

Answer 1

[Priyank Pandey]

Hi Aditya,

MATLAB does not have built-in support for creating pyramidal OME-TIFF files directly.

You can use additional tools, such as the Bio-Formats library, to achieve this. Refer the link below to know more about the toolbox:

Bioformats Image Toolbox - File Exchange - MATLAB Central (mathworks.com)

Regards

Priyank