Fiji 3D multi channel stitching - Was Re: Axiovision: Panorama and Multidimensional acquisition

[Daniel James White]

Dear Eric and others interested in panoramas or tile  stitching.

For stitching of overlapping tiles of z stack with multiple channels,
the Fiji plugins in he  plugins-stitching menu item , see
http://pacific.mpi-cbg.de/wiki/index.php/Stitching_2D/3D

These plugins take the overalpping image information and do a global registration,
not by where the stage thinks it was, but by the actual information in the image.

It gets the overlap right, if there is overlap, even if you dont know the spatial configuration of the tiles,
as it can figure it out by itself.

incidentally....the plugin's author is about to submit his thesis that included this stuff....

if you need help , just yell!

cheers

Dan




On Jul 1, 2010, at 7:01 AM, CONFOCALMICROSCOPY automatic digest system wrote:

> Date:    Wed, 30 Jun 2010 07:14:17 -0500
> From:    "Viereck, Friedhelm" <[hidden email]>
> Subject: Re: Axiovision: Panorama and Multidimensional acquisition
>
> - Commercial interest -
> Hi Eric,
>
> I'm working as a product manager for AxioVision...
>
> I'm sorry but there is no way to bring a multichannel image into a "Panor=
> ama
> generated" image, because the "Snap F2" button performs a snap of a singl=
> e
> channel only.
>
> Sorry for the inconvenience,
> Friedhelm
>
> On Wed, 30 Jun 2010 13:46:26 +0200, Eric Scarfone <[hidden email]> w=
> rote:
>
>> Hi List.
>> This is not a confocal question but I do not know where to find a better=
>
> goup of imaging experts!
>> We are trying to make mosaic images using the "Panorama" feature of Zeis=
> s
> Axiovision software (our mic does not have a motorized stage so this is
> manual). It works well, but I would like each frame of the mosaic to be a=
>
> multidimensional image (ie multiple fluorescence).
>> And I could not find a way to do that!
>> Any ideas?
>> Cheers
>> Eric
>>
>>
>> Eric Scarfone, PhD, CNRS,=20
>> Center for Hearing and communication Research=20
>> Department of Clinical Neuroscience=20
>> Karolinska Institutet=20
>>
>> Postal Address:=20
>> CFH, M1:02=20
>> Karolinska Hospital,=20
>> SE-171 76 Stockholm, Sweden=20
>>
>> Work: [phone],=20
>> Cell: [phone]=20
>> Fax: [phone]=20
>>
>> email: [hidden email]=20
>> http://www.ki.se/cfh/=20

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 )