compressed DICOM

[John T. Sharp]

I need to open compressed DICOM files in ImageJ. I don't know the compression method except it is said by the individual carrying out the compression to be lossless.

Anybody have a plugin or any program to do it or know of a source for downloading one?

TIA

[Gerald Veldhuijsen]

Hi,

I've got the same problem. As far as I know there's no plugin available
that can open it.
The problem is that these image are compressed using lossless JPEG
compression.
An imagereader for this is included in the Java Advanced Imaging api, but
this means writing your own plugin.

Gerald

[rmlang]

Dears TIA and Gerald,

Someone managed to create a plugin to open compressed dicom files?

I need this solution.

Thanks in advance,

Robert Mauro Lang

[ctrueden]

Hi Robert,

> Someone managed to create a plugin to open compressed dicom files?

The Bio-Formats Importer plugin
(http://www.loci.wisc.edu/ome/formats.html) now opens compressed DICOM
files. Please note that certain kinds of compression (i.e., lossless
JPEG) require that you also install the JAI ImageIO Tools native
library. Instructions for doing so can be found on the Bio-Formats web
site in the "Setting up native libraries" section.

Please let me know if you encounter any difficulties with it.

-Curtis

On Jan 16, 2008 6:24 AM, rmlang <[hidden email]> wrote:

> Dears TIA and Gerald,
>
> Someone managed to create a plugin to open compressed dicom files?
>
> I need this solution.
>
> Thanks in advance,
>
> Robert Mauro Lang
> --
> View this message in context: http://www.nabble.com/compressed-DICOM-tp1841759p14857153.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>

[rmlang]

Hi Curtis!

I need to write a Dicom Viewer with Java Web Start Technology
and a loci_tools.jar library is biggest (8,1Mb).

Today, my application is less than 2,0 Mb and is very big to use
with bad connections on brasilian internet.

I need only open a Dicom-Jpeg 2000 (loss-less and lossy) in imageJ
and isn't necessary other formats.

If you can help me with this, please reply!

Thanks in advance!

Robert Mauro Lang

[ctrueden]

Hi Robert,

> I need to write a Dicom Viewer with Java Web Start Technology
> and a loci_tools.jar library is biggest (8,1Mb).

The short answer:

Do not use loci_tools.jar with Web Start. Instead, use
bio-formats.jar, clibwrapper_jiio.jar and jai_imageio.jar. Note that
your clients will need to install the JAI ImageIO Tools into the JRE
used by Web Start in order to read lossless DICOM files.

The long answer:

Allow me to clarify the purpose of loci_tools.jar. This file is merely
a bundle of bio-formats.jar plus all its optional dependencies. It is
intended as a convenience (to simply installation as an ImageJ plugin,
for example), but is by no means the only solution for developers. If
you read the "Using Bio-Formats as a Java library" section of the web
site, you'll see that we recommend using bio-formats.jar as a separate
entity depending on your needs as a developer.

It has grown large because we have added support for several formats
that need large helper libraries (e.g., Imaris's new HDF format).
However, all of these additional libraries are optional -- Bio-Formats
has been coded using reflection so that it can both compile and run
without these optional libraries.

Regarding JNLP, I agree that serving loci_tools.jar directly to a Java
Web Start app is not the best approach, since every time Bio-Formats
is updated, it would need to feed another 8+ MB JAR file to the end
user. But Web Start is a case where you would keep the JARs separate
rather than bundling them together, since JNLP was designed to make
management of JAR dependencies trivial for the end user. You would
just keep bio-formats.jar and the optional dependencies all separate,
so that when bio-formats.jar changes, only a <1 MB JAR needs to be
updated.

At the risk of being overly verbose, using loci_tools.jar is exactly
equivalent to using bio-formats.jar with all of the following optional
libraries:

bufr-1.1.00.jar
clibwrapper_jiio.jar
grib-5.1.03.jar
jai_imageio.jar
mdbtools-java.jar
netcdf-4.0.jar
poi-loci.jar
slf4j-jdk14.jar
ome-java.jar
commons-httpclient-2.0-rc2.jar
commons-logging.jar
xmlrpc-1.2-b1.jar
omero-common.jar
omero-client.jar
forms-1.0.4.jar
loci_plugins.jar
ome-notes.jar

An up to date version of this list is explicitly enumerated in the
tools.libraries variable of the build.properties file of the
distribution:
https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/build.properties

Each of the libraries is only necessary for a specific task. For
example, you don't need poi-loci.jar unless you want to read
OLE2-based file formats. you don't need ome-java.jar (or
commons-httpclient-2.0-rc2.jar, commons-logging.jar, and
xmlrpc-1.2-b1.jar) unless you want to use Bio-Formats to connect to an
OME server. You don't need omero-common.jar or omero-client.jar unless
you want to connect to an OMERO server. You don't need
loci_plugins.jar unless you want to use the Bio-Formats ImageJ
plugins. Etc.

The Bio-Formats web site lists the purpose of many of these libraries.
 You can also read our notes about each in the Ant build.xml file
here: https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/build.xml#L169

As a developer, you have the option of packaging bio-formats.jar with
as many or as few of these libraries as you wish, to cut down on file
size, if file size is an issue for you. So you are free to make
whatever kind of "stripped down" version you wish. You could even
build a custom bio-formats.jar that excludes certain classes, if you
wish.

If you have any questions about packaging or distribution, feel free
to ask; I would be glad to help.

HTH,
Curtis

On Jan 16, 2008 2:03 PM, rmlang <[hidden email]> wrote:

> Hi Curtis!
>
> I need to write a Dicom Viewer with Java Web Start Technology
> and a loci_tools.jar library is biggest (8,1Mb).
>
> Today, my application is less than 2,0 Mb and is very big to use
> with bad connections on brasilian internet.
>
> I need only open a Dicom-Jpeg 2000 (loss-less and lossy) in imageJ
> and isn't necessary other formats.
>
> If you can help me with this, please reply!
>
> Thanks in advance!
>
> Robert
>
> --
> View this message in context: http://www.nabble.com/compressed-DICOM-tp1841759p14891635.html
>
> Sent from the ImageJ mailing list archive at Nabble.com.
>

[Nino Pereira]

Curtis,

FYI, I lurk on the ImageJ web site because I've started to use
it for my very simple needs. I'm sure I'll need help in the
future, and for this the ImageJ mailing list seems excellent.

I'd like to compliment you on your answer to Robert:

> The short answer:
>
> Do not use loci_tools.jar with Web Start. ,

followed up with a very helpful
> The long answer:
>
> Allow me to clarify the purpose of loci_tools.jar.

and suggestions for further reading.
> An up to date version of this list is explicitly enumerated in the
> tools.libraries variable of the build.properties file of the
> distribution:
> https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/build.properties

I sure wish that every help list group was as good as that from ImageJ.
>
Nino

[rmlang]

Dear Curtis,

Really you are right. I will do some tests with bio_format.jar and continue with messages in this post.
I think erroneously understood the use of these libraries.

Thank you for that clarification.

Best regards,

Robert Mauro Lang

[Veronica]

Thank you all for the nice post. I am new to java, and I am trying to make imageJ work for compressed dicom (JPEG2000). What I did is that after I installed imageJ, I put bio-formats.ar and loci_tools.jar, loci-common.jar and jai_imageip.jar under the imageJ\plugins\. However, it's still complaining about unable to open the file through LOCI\bio-format importer. Can you help?!