Bfopen.m of Bio-Formats MATLAB toolbox does not support 5D hyperstack?

bio-formats
imagej
matlab
image5d

#1

I’ve just realized that bfopen of Bio-Formats MATLAB toolbox does not support 5D hyperstack.

When I saved the sample image mitosis.tif in TIFF or OME.TIFF, bfopen output treated 2 channels, 5 slices and 51 frames as 510 series.

Honestly, I’m rather disappointed by this. The data structure does not really give us a room to fix this.

Is there a workaround? Can bfGetReader handle hyperstack well?


#2

bfGetReader and bfGetPlane seem to be the solution.

https://docs.openmicroscopy.org/bio-formats/5.8.2/developers/matlab-dev.html


#3

Check out Matlab Central file exchange

This works for me with 5d stacks.


#4

Thanks! I was going to create my own. It uses bfGetReader as expected.


#5

Nice to hear you like it.