Re: IMAGEJ Digest - 1 Mar 2011 to 2 Mar 2011 (#2011-58)

[Daniel James White]

Hi Mats,

On Mar 3, 2011, at 6:00 AM, IMAGEJ automatic digest system wrote:

>
> Date:    Wed, 2 Mar 2011 23:09:57 +0100
> From:    Mats Leif Moskopp <[hidden email]>
> Subject: Re: google summer of codes
>
> Dear ImageJ-development team,
>
> my name is Mats Moskopp. I'm a 21 years old student of medicin in Dresden
> (Germany).
> I'd like you to ask if you would like to participate at the google
> summer of code, about which you are surely informed already. (Google gives
> scholarships to students, who help to develop open-source
> projects. (
> http://www.google-melange.com/document/show/gsoc_program/google/gsoc2011/timeline
> ))

Its a good thing to do!

>
> I have already a few ideas which can
> improve imagej. I'm using it very often for my doctoral thesis.
> - the editor and the whole uploading system for self-written makros is
> not able to work in an easy way. At this point it could be useful to think
> about a better editor which allows you to work inside imagej on macros. Next
> thing is that the
> debugging is not "user-friendly". Often mistakes are marked twice ...

You are in Dresden, and so are we....
we are several core developers of the Fiji project - Fiji is just imageJ - batteries included.

One of the batteries that Johannes has ncluded is exactly what you are talking about.
The Fiji Script editor speaks ImageJ Macro lang, java, java script, beanshell, clojure....
It has syntax highlighting, and effectively gives you a nice script / plugin development
environment that is tightly integrated in the ImageJ.
Edit code, then run it and debug it.

see
http://pacific.mpi-cbg.de/wiki/index.php/Using_the_Script_Editor
 

> - For many reasons it could be useful to work with different Logs. I think
> about improved interfaces for data processing.

do you mean different kinds of log output window for imageJ?

> - i'd like to create a few makros/filters about Shape-detection
> which could be really useful for many kinds of other projects. So that you
> could detect certain forms in the pictures and characterise them (like
> plugins which deciphers digital informations in the images like bar-codes).

Feel free to do that within the Fiji environment and build system,
or use elcipse if you like...

get the whole source code and build it (its very easy) , then stasrt hacking away!
http://pacific.mpi-cbg.de/wiki/index.php/Git_mini_howto


these kind of things would be a nice addition tothe package of plugins bundled to Fiji users in the Fiji updater.

>
> Maybe you have other ideas which can be solved or fixed. Or a project
> which is not jet realisated. - Please feel free to propose me something.

there are lots of imageJ people here at MPI-CBG (near the uni klinikum)

why dont you come and say Hi!
We would be very please to talk to another imageJ fan in Dresden!

cheers

Dan



>
> Unfortunately we have not much time, because the the deadline for mentoring
> organizations is very soon (11. March 2011).
>
> Greetings
> Mats Moskopp

Dr. Daniel James White BSc. (Hons.) PhD
Senior Microscopist / Image Visualisation, Processing and Analysis
Light Microscopy and Image Processing Facilities
Max Planck Institute of Molecular Cell Biology and Genetics
Pfotenhauerstrasse 108
01307 DRESDEN
Germany

[phone] (German Mobile)
[phone] (Work phone at MPI-CBG)
[phone] (Fax MPI-CBG LMF)

http://www.bioimagexd.net  BioImageXD
http://pacific.mpi-cbg.de                Fiji -  is just ImageJ (Batteries Included)
http://www.chalkie.org.uk                Dan's Homepages
https://ifn.mpi-cbg.de  Dresden Imaging Facility Network
dan (at) chalkie.org.uk
( white (at) mpi-cbg.de )

[Toby Cornish]

Do you know what the uncompressed size of these images is (should be less than 4GB, I think)? I have this same problem opening large Jp2s (I have 12GB RAM), which has led me to use other solutions such as MatLab and the Kakadu library for dealing with large Jp2s. Even then I try not to use the full-sized image where possible, but my Jp2s are more like 200-300MB. If I want to work interactively with the full-resolution image, I will use a viewer specifically designed for dealing with very large images (such as a whole slide image viewer). Sorry if that is not very helpful.

I suggest contacting the LOCI group directly as they are usually very helpful when their library has issues. If this problem isn't the fault of their library, they are usually pretty quick to point out where the problem exists.

Toby

Date:    Wed, 2 Mar 2011 12:26:12 -0800
From:    Anda Cornea <[hidden email]>
Subject: JP2 memory limit?

Hello!

I am trying to open jp2 images of 20-30MB and get the error message below.  I can open tiffs of 100MB and more.  I can open jp2 of 2-5MB.  This is true on a 64 bit just updated to latest ImageJ (Maximum memory 4000 and 4 parallel threads) and LOCI, and on my regular 32 bit 1.44p(Maximum memory 618 MB and 2 parallel threads, from which I copy the message.

[Anda Cornea]

Uncompressed size is in the 100s MB.  I could use PaintShop Pro to open a jp2 file resistant to ImageJ and export it as a tif at 600MB.  

What whole slide image viewer are you using?  I am very interested in that.

Thanks,

Anda

Anda Cornea, Ph.D.
Director of the Imaging and Morphology Core
Oregon National Primate Research Center
503-690-5293

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Toby Cornish
Sent: Thursday, March 03, 2011 7:15 AM
To: [hidden email]
Subject: Re: IMAGEJ Digest - 1 Mar 2011 to 2 Mar 2011 (#2011-58)

Do you know what the uncompressed size of these images is (should be less than 4GB, I think)? I have this same problem opening large Jp2s (I have 12GB RAM), which has led me to use other solutions such as MatLab and the Kakadu library for dealing with large Jp2s. Even then I try not to use the full-sized image where possible, but my Jp2s are more like 200-300MB. If I want to work interactively with the full-resolution image, I will use a viewer specifically designed for dealing with very large images (such as a whole slide image viewer). Sorry if that is not very helpful.

I suggest contacting the LOCI group directly as they are usually very helpful when their library has issues. If this problem isn't the fault of their library, they are usually pretty quick to point out where the problem exists.

Toby

Date:    Wed, 2 Mar 2011 12:26:12 -0800
From:    Anda Cornea <[hidden email]>
Subject: JP2 memory limit?

Hello!

I am trying to open jp2 images of 20-30MB and get the error message below.  I can open tiffs of 100MB and more.  I can open jp2 of 2-5MB.  This is true on a 64 bit just updated to latest ImageJ (Maximum memory 4000 and 4 parallel threads) and LOCI, and on my regular 32 bit 1.44p(Maximum memory 618 MB and 2 parallel threads, from which I copy the message.