imagej centric application?

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imagej centric application?

Zummy
ImageJ list:

My understanding from my boss is that he wants me
to explore making ImageJ one of the main parts of our
application.  Right now, we just send images to ImageJ
through the ImageJ API.

We have a view only application that has a large relational
database behind it.  Domain specific features shown as as
circles, points, boxes, lines appear in x,y coordinates on the
images.  These features are tracked through a spatial coordinate,
z, and also through time.  The images are classified with a variety
of attributes, and we need to provide better ways of searching for
images and image sets.  We would like to load partial sets, but
allow for navigation to the rest of the set (lazy loading).  Also,
we have graphs, tables, and metadata that we would like to show
in the application.

We are interested in image frameworks that make heavy use of
the relational databases.  How well does ImageJ integrate with
images delivered over the web from a database or file, as well as direct
JDBC connection to the database?  Are there example database
schemas or frameworks for dealing with image and relational
data like the above?

A possible future might be that user's will want to save images
they've worked on back to the database, in a user area.

So I will be investigating the use of ImageJ with these features
in mind.  Any help or guidance in the API or ideas would be
appreciated.  If I were to develop an application using ImageJ
as a core, what extension APIs should I be looking at?

John
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Re: imagej centric application?

Albert Cardona
John,

I am developing one such ImageJ application that uses a PostgreSQL database
for everything, from saving the images themselves to store user-outlined
structures and other data for the purpose of 3D modelling.

For this application I've made several test plugins such as the
PostgreSQL_.java plugin which I have posted at

http://www.pensament.net/java/other_plugins.html

which you may find useful.

Beware there is a bug with it: the image_name column is not really editable
since there is a query where it is used directly (haven't found the time to
correct it and upload it, and I came across the problem maybe 2 days ago).

In my experience, the JDBC driver works fantastically well if you compile it
yourself for your specific system from the PostgreSQL sources. Otherwise the
binary streams may fail (for instance when using the same JDBC .jar driver in
different OSes).

Albert

--


Albert Cardona
Institute of Neuroinformatics     Tel : +41 1 635 3052
University/ETH Zurich             Fax : +41 1 635 3053
Winterthurerstrasse 190           acardona (at) ini phys ethz ch
Zurich 8057, Switzerland          www.ini.unizh.ch
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Re: imagej centric application?

Abramoff-Michael
In reply to this post by Zummy
Webscreen, a (crossplatform) image telediagnosis framework  based on
ImageJ and Tomcat uses SQL. I decided early on to do the persistency in
SQL, and use the file system to store the images - so there is an SQL
images table with all the info for the image (including DICOM fields)
and a pointer to the location in the file system. Webscreen has been
running robustly for the last 4 years on both Linux and Windows XP
installations.

I put a lot of thought into the decision whether to store the images as
BLOBs in SQL or use the filesystem. There was no real evidence for
either choice at that moment. I read somewhere that filesystems are
designed to efficiently store large files, and SQL implementations may
be less effcient. This may have changed ovet the last 4 years,
obviously.
To remain flexible, I made a single class that encapsulates the reading
writing and streaming of the images: replacing the class would allow to
use the SQL datastorage (BLOBS) for the images instead of the
filesystem.

Hope this helps,

Michael Abramoff

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
John Carlson
Sent: Friday, August 19, 2005 7:44 PM
To: [hidden email]
Subject: imagej centric application?

ImageJ list:

My understanding from my boss is that he wants me to explore making
ImageJ one of the main parts of our application.  Right now, we just
send images to ImageJ through the ImageJ API.

We have a view only application that has a large relational database
behind it.  Domain specific features shown as as circles, points, boxes,
lines appear in x,y coordinates on the images.  These features are
tracked through a spatial coordinate, z, and also through time.  The
images are classified with a variety of attributes, and we need to
provide better ways of searching for images and image sets.  We would
like to load partial sets, but allow for navigation to the rest of the
set (lazy loading).  Also, we have graphs, tables, and metadata that we
would like to show in the application.

We are interested in image frameworks that make heavy use of the
relational databases.  How well does ImageJ integrate with images
delivered over the web from a database or file, as well as direct JDBC
connection to the database?  Are there example database schemas or
frameworks for dealing with image and relational data like the above?

A possible future might be that user's will want to save images they've
worked on back to the database, in a user area.

So I will be investigating the use of ImageJ with these features in
mind.  Any help or guidance in the API or ideas would be appreciated.
If I were to develop an application using ImageJ as a core, what
extension APIs should I be looking at?

John
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