Batch Converting of z-stacks

[albot]

Hi all,

I received a question where I do not know whether you think it could easiliy be solved with OMERO or maybe also ImageJ.

>
Essentially I want to take my 230 *.oib files (which contain the individual tiffs of a stack) and have those converted into a jpeg (a z-stack made from the tiffs in the oib file) as a batch...

Normally, I do this in imagej on individual files by 1) opening oib file in imagej, 2) convert into a Z-stack (Z projection) of max intensity, and 3) saving generated image as a jpeg (I usually convert the image from 16-bit to 8-bit first before saving, but maybe that is not necessary in omero)
>

Any comments from the community would be appreciated.

Cheers Alex

[wmoore]

Hi Alex,

One solution in OMERO is to use the "Combine Images" script. See https://www.openmicroscopy.org/site/sup ... ine-images

You'd probably want to choose "Manually Define Dimensions" and then choose "Z" as your "Dimension 1".

This should do what you want.

The only drawback to doing this in OMERO is that you have to do a lot of imports, then delete the tiffs when you're done.

Will.

[wmoore]

On re-reading your post, I'm not sure I've understood you correctly.

You're not trying to create a Z-stack image in OMERO, but you want a single jpeg Z-projection (or multiple jpegs?) from a series of oib files?

You can "Batch Export" a single or multiple images as jpegs, choosing Z-projection or every z-plane from each, using the "Export Script" > "Batch Image Export".

Is that what you wanted?

Will.

[albot]

Hey Will,
The "Export Script" > "Batch Image Export" suggestion worked fine for my colleagues...

Thanks!

Cheers Alex