Non-default ordering in Stacks to Hyperstacks... command with virtual stacks

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Non-default ordering in Stacks to Hyperstacks... command with virtual stacks

Jeff Hardin-2
Hi all,
I hope you’re all doing well.

Trying to make the most of my COVID-restricted time, I’m trying to import some really old 4d movies from my lab that were made using some QuickTime for Java-based  plugins I wrote many years ago. As QTJ is deprecated on modern 64-bit systems (in particular, MacOS Catalina and beyond), I’m trying to use the ffmpeg plugin in Fiji to import them. They are large, so it is far more efficient to import each movie as a Virtual Stack.

The initial import as a virtual hyperstack works great with many movies. Unfortunately, the ordering of the images in the original is xyctz. This means that when I try to convert to a Hyperstack with the correct ordering, ImageJ tells me that the Stacks to Hyperstacks…  command must use the default ordering when using virtual stacks..

I’m wondering if anyone knows of a workaround to execute the equivalent of the Stacks to Hyperstacks... command on virtual stacks without the default ordering (xyczt). If no such workaround exists, I’d like to request that a future update to ImageJ add this capability.

Thanks to everyone who makes this even close to possible with 20-yr old data!

Best regards,
Jeff

******
Jeff Hardin
Raymond E. Keller Professor and Chair
Department of Integrative Biology
Faculty Director, Biology Core Curriculum
University of Wisconsin
1117 W. Johnson St.
Madison, WI 53706
voice: (608) 262-9634
fax: (608) 262-7319
email: [hidden email]
web page: http://worms.zoology.wisc.edu


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Re: Non-default ordering in Stacks to Hyperstacks... command with virtual stacks

Wayne Rasband-2
Starting with the ImageJ 1.53d10 daily build, the Stack to Hyperstack command, when the order is not xycvt, works with virtual stacks created by Import>Image Sequence, Import>AVI and Import>TIFF Virtual Stack. It does not work with plugins that extend VirtualStack, such the ffmpeg plugin, but you can work around this by saving in TIFF format and re-opening as a TIFF Virtual Stack.

-wayne


> On Jun 29, 2020, at 4:51 PM, Jeff Hardin <[hidden email]> wrote:
>
> Hi all,
> I hope you’re all doing well.
>
> Trying to make the most of my COVID-restricted time, I’m trying to import some really old 4d movies from my lab that were made using some QuickTime for Java-based  plugins I wrote many years ago. As QTJ is deprecated on modern 64-bit systems (in particular, MacOS Catalina and beyond), I’m trying to use the ffmpeg plugin in Fiji to import them. They are large, so it is far more efficient to import each movie as a Virtual Stack.
>
> The initial import as a virtual hyperstack works great with many movies. Unfortunately, the ordering of the images in the original is xyctz. This means that when I try to convert to a Hyperstack with the correct ordering, ImageJ tells me that the Stacks to Hyperstacks…  command must use the default ordering when using virtual stacks..
>
> I’m wondering if anyone knows of a workaround to execute the equivalent of the Stacks to Hyperstacks... command on virtual stacks without the default ordering (xyczt). If no such workaround exists, I’d like to request that a future update to ImageJ add this capability.
>
> Thanks to everyone who makes this even close to possible with 20-yr old data!
>
> Best regards,
> Jeff

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