FIJI-Bioformats in headless mode

[Lachie]

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

[wmoore]

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.

[crueden]

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...

[Lachie]

Hi Curtis,

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

-Lachie

[sbesson]

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