Re: Hosted version of ImageJ

Posted by Jerome Mutterer-3 on
URL: http://imagej.273.s1.nabble.com/Hosted-version-of-ImageJ-tp5007303p5007307.html

Dear Seth, dear ImageJ group
related to your question, I uploaded yesterday a page on the wiki that
describes how how can run ImageJ as a Galaxy tool.
Galaxy is an open, web-based platform. You can upload data to a Galaxy
server, and then process it with Galaxy tools. These tools have inputs and
outputs, and I created some tools that take tif images as input and return
tif images as output. Then you can also chain Galaxy tools as workflows,
save the workflows and run them later on different input images.
So far it is just a proof of concept, and there is a lot a space for
improvements:
- the example tools are invoking python scripts that call ImageJ with the
-batch option and as such do not work if totally headless (but it works on
the mac). Fiji certainly can help there.
- ImageJ is launched for each step in a workflow, which results in rather
slow processing. A tool that would start an instance of ImageJ on the
server that would then be reused by other tools would be nice.
- so far I have only TIF as input and TIF as output. It would be useful to
have Roisets or Results tables as output, so that you could also chain with
existing Galaxy tools.
But the overall concept works.
See
http://imagejdocu.tudor.lu/doku.php?id=howto:working:setting_up_ij_tools_in_galaxy
for
more details.

I know there are other similar or related projects (work-flow-pipes, alida,
knime) but we tried Galaxy because it is already widely used for
bioinformatics.

Sincerely,

Jerome.


On 15 April 2014 06:15, Seth Daugherty <[hidden email]> wrote:

> I'm considering building an "ImageJ for the cloud" that would implement
> ImageJ functionality in a web browser and perform image processing on a
> server. Think AWS for ImageJ.
>
> This service would allow users ad-hoc access to run their computations
> servers with more power than they would have other wise. (This would
> possibly include the ability to distribute processing across a cluster of
> servers.)
>
> Is anybody interested in something like that? What sort of features would
> you like to see?
>
> Thanks!
> Seth
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
Jerome Mutterer
CNRS - Institut de biologie moléculaire des plantes
 12, rue du Général Zimmer
67084 Strasbourg Cedex
T 0367155339
www.ibmp.cnrs.fr

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