Re: akoya file format

Posted by Mike Nelson on
URL: http://confocal-microscopy-list.275.s1.nabble.com/akoya-file-format-tp7591754p7591762.html

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Hi Simon,

Just to add a quick note on to what Ajay mentioned about QuPath:
"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."
The most exciting part for local labs has been that you can stitch together
multiple fields of view (*unmixed tif files* exported from InForm) into
pyramidal whole slide images.
Specific script by Pete Bankhead can be found here:
https://gist.github.com/petebankhead/b5a86caa333de1fdcff6bdee72a20abe

I second checking and or posting on the image.sc forum - I am a big fan :)

And, in relation to Sripad's comment, do you no longer have access to
InForm?

Cheers,
Mike


On Fri, Jan 22, 2021 at 7:45 AM Zalavadia, Ajaykumar <[hidden email]>
wrote:

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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: [phone] | email: [hidden email]<mailto:[hidden email]>
>
>
> From: Confocal Microscopy List [mailto:[hidden email]]
> On Behalf Of Watkins, Simon C
> Sent: Friday, January 22, 2021 7:57 AM
> To: [hidden email]
> 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
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