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FIJI-Bioformats in headless mode

Historical discussions about the Bio-Formats library. Please look for and ask new questions at https://forum.image.sc/tags/bio-formats
Please note:
Historical discussions about the Bio-Formats library. Please look for and ask new questions at https://forum.image.sc/tags/bio-formats

If you are having trouble with image files, there is information about reporting bugs in the Bio-Formats documentation. Please send us the data and let us know what version of Bio-Formats you are using. For issues with your code, please provide a link to a public repository, ideally GitHub.

FIJI-Bioformats in headless mode

Postby Lachie » Wed Nov 18, 2015 11:44 pm

Hi All,

I've started working on running FIJI in headless mode (can you see where this is going?) on either local cluster or on the cloud but am running into some issues.

I've seen online that bioformats macro extensions don't work in headless mode except for the most basic
"Ext.openImagePlus()". Is there a work-around that would allow me to run some of the other extension commands (like setSeries, or accessing the metadata, or opening a subimage?

Thanks,
-Lachie
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Re: FIJI-Bioformats in headless mode

Postby wmoore » Mon Nov 23, 2015 10:21 am

Hi Lachie,

Apologies for the delay in replying.
You might get a quicker response by asking this question on the ImageJ e-mail lists.

Regards,

Will.
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Re: FIJI-Bioformats in headless mode

Postby crueden » Mon Nov 23, 2015 4:04 pm

In particular, I'd recommend posting at http://forum.imagej.net/. There are quite a few responsive and helpful experts there!

Responding to your query is on my to-do list, but my to-do list is pretty long these days...
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Re: FIJI-Bioformats in headless mode

Postby Lachie » Wed Nov 25, 2015 3:09 am

Hi Curtis,

Thanks for the heads up. I'll post over on imagej forums too.

-Lachie
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Re: FIJI-Bioformats in headless mode

Postby sbesson » Wed Nov 25, 2015 7:16 am

For cross-linking reference, the corresponding Fiji thread is at http://forum.imagej.net/t/bioformats-in ... s-mode/410.
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