[Insight-users] C elegans microscopy and stitching

[Dan White]

Hi Darren,

I think the basic tools are there in ITK  for sure,
its a question of implementation.

A good place to do that would be within BioImageXD project,
as a lot of the hard work is already done.,
and it is a Microscopy specific application using ITK and VTK via  
pytthon wrapppers.


2D and 3D visualisation , time series, multiple data channels/colours
basic filters, etc etc.  are already there.

You just need to decide what methods to use,
write the GUI in wxPython and drop it into BioImageXD.

My colleague also just made a really good 3D stitching pluging for  
imageJ.
The same ideas could probably be implemented in ITK/BioImageXD
That tool will be released in the fairly near future and will be open  
source of course.

If you want to join in with development/implementation of ITK tools
in BioImageXD, then just let me know.

THe source code is on the svn server at sourceforge,
just look at the bioimagexd.net website.

We are also working on C elegans microscopy here at MPI-CBG.
What microscopes are you using?
We have a SPIM prototype which works great for C elegans.

cheers

Dan



On Aug 9, 2008, at 6:00 PM, insight-users-request at itk.org wrote:

> Message: 1
> Date: Fri, 8 Aug 2008 18:05:56 -0700
> From: "Darren Weber" <darren.weber.lists at gmail.com>
> Subject: [Insight-users] microscopy stacks and stitching
> To: insight-users at itk.org
> Message-ID:
> 	<b808b3510808081805o765b206pf260014833d3c551 at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> I'm working with flourescent microscopy data for C. elegans.  The  
> data for
> an animal is acquired in sections (say 10 sections), each section  
> contains
> stacks of 100+ images of about 1024x1024.  The data can be anything  
> from
> 8bit to 16bit and various formats (.tiff seems to be a common export
> option).
>
> I just read with some interest this news item:
> http://www.kitware.com/company/news/nobel-prize.html
>
> Are the tools for stitching stacks available in the open-source code  
> for
> ITK?
>
> Best, Darren

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


New Mobile Number!!!

+49 (0)15114966933 (German Mobile)
+49  (0)351 210 2627 (Work phone at MPI-CBG)
+49  (0)351 210 1078 (Fax MPI-CBG LMF)

http://www.bioimagexd.net
http://www.chalkie.org.uk
dan at chalkie.org.uk
( white at mpi-cbg.de )