Posted by
Zalavadia, Ajaykumar on
URL: http://confocal-microscopy-list.275.s1.nabble.com/akoya-file-format-tp7591754p7591756.html
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Simon,
Bio-Formats Command Line Tools supports converting qptiff to ome.tiff, bio-fromats seems to carryover metadata (channel names and spatial resolution) nicely.
A simple command like this should work:
bfconvert input.qptiff output.ome.tiff
There other flags you can pass while converting depending on your requirements, such as:
-noflat -bigtiff -tilex 512 -tiley 512 -compression LZW -pyramid-resolutions 4 -pyramid-scale 2
If the channels in your qptiff have cross talks and plenty of auto fluorescence then it might be better to unmix them in to component data using inForm first. You can merge component images using something like QuPath. On a side note: QuPath works very well with qptiff files, it uses bio-formats to read qptiff files. It should also be possible to write a script in QuPath to batch convert files.
I have found Image.sc<
https://forum.image.sc/search?q=bfconvert> forums to be very resourceful for discussions related to ome.tiff conversion and QuPath<
https://qupath.github.io/>.
Best,
Ajay Zalavadia, Ph.D.
Imaging Specialist, Imaging Core | Lerner Research Institute
9500 Euclid Avenue NB10 | Cleveland, OH 44195
Phone: 216-444-8045 | email:
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Subject: [EXT] akoya file format
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Colleagues, has anyone developed or have a solution for porting data sets from the Akoya platform (specifically the Vectra in our case) to an OME TIFF?
We have been given the option or rescanning a ton of slides on one of our systems or finding a way to convert previously scanned data
Thanks for the wisdom and of course stay safe!
S
Simon C. Watkins Ph.D
Distinguished Professor and Vice Chair Cell Biology
Professor Immunology
Director Center for Biologic Imaging
University of Pittsburgh
Bsts 225 3550 terrace st
Pittsburgh PA 15261
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