Hosted version of ImageJ

[Seth Daugherty]

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

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[Lalit Saxena]

Data Security
Data Accessibility
Huge data Storage
Timely data Management


Would we promising areas in which one has to think while working on Cloud methodology.



-----Original Message-----
From: Seth Daugherty <[hidden email]>
To: IMAGEJ <[hidden email]>
Sent: Mon, Apr 14, 2014 11:24 pm
Subject: Hosted version of ImageJ


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

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

 

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[Jerome Mutterer-3]

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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[David Gene Morgan]

Very cool.  For those of you who don't yet know about Galaxy, take a
look at the website (http://galaxyproject.org/) and think about whether
a Galaxy-like server for your specific field or applications would be
useful.

On 04/15/2014 04:19 AM, Jerome Mutterer wrote:

> 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
>>
>
>
>

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                  David Gene Morgan
              Electron Microscopy Center
                   047D Simon Hall
                   IU Bloomington
                812 856 1457 (office)
                812 856 3221 (3200)
             http://bio.indiana.edu/~cryo

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