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Bio-formats opening the wrong colormaps in Matlab

Historical discussions about the Bio-Formats library. Please look for and ask new questions at https://forum.image.sc/tags/bio-formats
Please note:
Historical discussions about the Bio-Formats library. Please look for and ask new questions at https://forum.image.sc/tags/bio-formats

If you are having trouble with image files, there is information about reporting bugs in the Bio-Formats documentation. Please send us the data and let us know what version of Bio-Formats you are using. For issues with your code, please provide a link to a public repository, ideally GitHub.

Bio-formats opening the wrong colormaps in Matlab

Postby kitxiniti » Mon Jul 24, 2017 1:09 pm

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
kitxiniti
 
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Re: Bio-formats opening the wrong colormaps in Matlab

Postby dgault » Mon Jul 31, 2017 3:55 pm

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
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dgault
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