[Insight-users] ITK for fluorescence microscopy - BioImageXD

[Badri Roysam]

While we are on this topic, there is an aspect of BioFormats & OME that is worth thinking
about. This is the OME-TIFF format. Basically, all the microscope metadata is saved in
a microscope-independent format as a XML file within the TIFF file's text field. I 
believe this to be a valuable capability, since we often need to access metadata. At the
very least, we need voxel size along x, y, and z axes.


Badri Roysam
Professor, Department of Electrical, Computer and Systems Engineering
Associate Director, NSF Center for Subsurface Sensing & Imaging Systems (CenSSIS ERC)
Co-Director, Rensselaer Center for Open Source Software
Rensselaer Polytechnic Institute
110 8th Street, Troy, New York 12180-3590, USA.
Office(JEC 7010): 518-276-8067, Assistant: 518-276-8525, Lab(JEC 6308): 518-276-8207, Fax: 518-276-8715
Email: roysam at ecse.rpi.edu, Web: http://www.ecse.rpi.edu/~roysam



----- Original Message -----
From: Daniel James White [mailto:white at mpi-cbg.de]
To: alex gouaillard [mailto:Alexandre_Gouaillard at hms.harvard.edu]
Cc: ITK [mailto:insight-users at itk.org]
Subject: Re: [Insight-users] ITK for fluorescence microscopy - BioImageXD


> 
> On May 12, 2009, at 12:54 PM, alex gouaillard wrote:
> >>
> >> The vtkLSM Reader was a lot of work, because the LMD510 file format  
> >> is
> >> a real pig (but at least its fast) ...
> >>
> >> writing file format readers for VTK is a good thing... but better to
> >> put effort into enhancing the
> >> LOCI Bio-Formats java library and use that for microscopy image and
> >> meta data IO.
> >> That way the wheel is not reinvented over and over, and we can all
> >> benefit from each others work more easily.
> >
> > agreed, but I thought that was an ongoing project in the community?
> > I remember a long thread around january about this?
> 
> not sure what you mean....
> yes there was a long thread about it...
> 
> for my money, the right thing to do is to develop bio-formats
> and its integration into other projects
> rather than writing the same file readers for every project.
> 
> >
> >>
> >>
> >> BXD might well move to java wrapped VTK/ITK from python in the
> >> future,  primarily for platform independence reasons: No 64 Bit  
> >> Carbon
> >> on OSX.
> >> That would also allow a direct interface with Fiji-ImageJ , which
> >> would be very cool.
> >
> > Why not using Cocoa instead of carbon if you want 64 bits?
> > Java rapping is interesting on hits own, of course, for other reasons.
> 
> wxPython  (for out GUI) only works with Carbon on OSX,
> and the native wxAqua port of wxWindows/Widgets is nowhere near  
> production ready...
> 
> so with wxPython on OSX we are stuck with 32 bit,
> unless we make the effort to bring wxAqua up to scratch,
> and thats a big job.
> 
> Switching to java might be easier and also have other long term  
> benefits,
> as you allude to.
> 
> D
> 
> 
> 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
> 
> +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 	BioImageXD
> http://pacific.mpi-cbg.de Fiji 	Fiji is just ImageJ - Batteries Included
> http://www.chalkie.org.uk
> dan at chalkie.org.uk
> ( white at mpi-cbg.de )
> 
> 
> 
> 
> 
> 
> 
> 
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