Posted by
Sripad Ram-2 on
URL: http://confocal-microscopy-list.275.s1.nabble.com/akoya-file-format-tp7591754p7591757.html
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Hi Simon,
Are you referring to the qptiff images or the im3 files? QPTiFF is a newer
file format that can be ported/read relatively easily. If the data was
generated on Vectra 3 then more than likely you have im3 files which store
the MSI data. I have had good success in reading the raw images from im3
files using the bioformat plugin in Matlab (at least I used to many years
ago). However, I have not been successful in reading the metadata from im3
files.
The IM3 files only store the raw MSI data not the spectrally unmixed
component images. So if you want to do unmixing then you'd have to
implement that yourself. The unmixing algorithm is not difficult to
implement but you will need metadata such as the wavelength bands, step
size of the LCTF, acquisition settings, etc., which is all locked in the
im3 file.
Thanks.
Sripad
On Fri, Jan 22, 2021 at 4:57 AM Watkins, Simon C <
[hidden email]>
wrote:
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>
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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
>
[hidden email]<mailto:
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> Www.cbi.pitt.edu<
http://www.cbi.pitt.edu/>
> phone:412-352-2277
>