Open Microscopy Environment

Hello everybody,

I have been using Bio-Formats in Matlab (i.e. bfopen function) to open multichannel time-lapsed tiff files from a .lif (Leica format) file. Using "bfopen" I only get one colormap even though I might have 2 or 3 channels with different color maps.

Anybody has a solution for this? or has experience similar issues?

Funny enough, if I save the tif file with the red channel in the foreground, bfopen only sees a red colormap in all channels. Instead, if i save the same file with the green channel in the foreground bfopen only see a green color map. I can open both tif files in Fiji and all the channels with the correct colormaps are there. I use bio-formats in Fiji to actually open and save the tiff files from the original lif file.

To me it seems that there is an issue with the bfopen function in Matlab, but i might be wrong.

Best

Hi,

Thank you for raising the issue with us, this does indeed look likely to be an issue in the bfopen.m file. I have opened a Trello card on the Bio-Formats inbox to further investigate and put a fix in place: https://trello.com/c/dVEIbyRH/166-matla ... -colormaps

David Gault