SDT files and Matlab

[Peter Humphreys]

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Hugin works well for 2d.
Peter

> *****
> To join, leave or search the confocal microscopy listserv, go to:
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>
> Does anyone have a favorite free/shareware image stitching program they'd like to share?  I have never attempted it in ImageJ either, is there a plug in?
>
> I am only trying to stitch together a few images right to left, not in both directions.
>
> Thanks for anything you have to share.
>
> Christian

[Steffen Dietzel]

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On 15.11.2010 20:37, Pedro Almada wrote:
>
> I've had great success with the 2D/3D stitching plugin for ImageJ that is
> included in the FIJI package:
> http://pacific.mpi-cbg.de/wiki/index.php/Stitching_2D/3D
>

I second that. I use this plugin in "normal" ImageJ, 64bit-Windows.
Stitching 200 MB 3D stacks together is not a problem. I didn't have a
case where it wouldn't work if the edges to be stiched where marked as
ROI. In many cases it also works without ROIs but for stacks it then
takes noticeably longer and needs more RAM.

The only drawback is that the stiching-plugin is not compatible with
newer versions of the LOCI Bioformatimporters, i.e. if both are
installed LOCI doesn't work while stitching does. (so you have to get
the stitching folder out of your plugins folder and restart ImageJ to
bioimport.)

Steffen

--
------------------------------------------------------------
Steffen Dietzel, PD Dr. rer. nat
Ludwig-Maximilians-Universität München
Walter-Brendel-Zentrum für experimentelle Medizin (WBex)
Head of light microscopy

Mail room:
Marchioninistr. 15, D-81377 München

Building location:
Marchioninistr. 27,  München-Großhadern

[Christian-103]

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I will check it out, along with FIJI the ImageJ package.  Thanks for all the input.



--- On Tue, 11/16/10, Mario Emmenlauer <[hidden email]> wrote:

From: Mario Emmenlauer <[hidden email]>
Subject: Re: image stitching
To: [hidden email]
Date: Tuesday, November 16, 2010, 1:32 AM

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Hi,

On 11/15/2010 08:46 PM, Mark Cannell wrote:
>
> See also:
>
> http://www.xuvtools.org/doku.php

XuvTools is neat because it can work manual or fully automatic, so you
can always fine-tune if something goes wrong. The newest version (beta)
can also read files via Bio-Formats library, so its worth looking at.
It will only stitch "real" 3D though, so stacks with more than 4 planes.
Thats a bug that the developers (meaning 'me') meant to fix for quite
a while now...

All the best,

    Mario

> Cheers
>
> On 16/11/2010, at 8:37 AM, Pedro Almada wrote:
>>
>>
>> I've had great success with the 2D/3D stitching plugin for ImageJ that is
>> included in the FIJI package:
>> http://pacific.mpi-cbg.de/wiki/index.php/Stitching_2D/3D
>>
>> On 15 November 2010 19:35, Cammer, Michael <[hidden email]>wrote:
>
>> sts.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
>>> *****
>>>
>>> If you have Photoshop CS3 or more recent, it has a nice Photomerge option
>>> in the File menu.
>>> -Michael
>>>
>>> -----Original Message-----
>>> From: Confocal Microscopy List [mailto:[hidden email]]
>>> On Behalf Of Christian
>>> Sent: Monday, November 15, 2010 2:33 PM
>>> To: [hidden email]
>>> Subject: image stitching
>>>
>>> *****
>>> To join, leave or search the confocal microscopy listserv, go to:
>>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
>>> *****
>>>
>>> Does anyone have a favorite free/shareware image stitching program they'd
>>> like to share?  I have never attempted it in ImageJ either, is there a plug
>>> in?
>>>
>>> I am only trying to stitch together a few images right to left, not in both
>>> directions.
>>>
>>> Thanks for anything you have to share.
>>>
>>> Christian
>>>
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>

[Daniel James White]

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Hi Stitchers,

On Nov 17, 2010, at 7:01 AM, CONFOCALMICROSCOPY automatic digest system wrote:

>
> Date:    Tue, 16 Nov 2010 16:48:31 +0100
> From:    Steffen Dietzel <[hidden email]>
> Subject: Re: image stitching
>
>
> On 15.11.2010 20:37, Pedro Almada wrote:
>>
>> I've had great success with the 2D/3D stitching plugin for ImageJ that is
>> included in the FIJI package:
>> http://pacific.mpi-cbg.de/wiki/index.php/Stitching_2D/3D
>>
>
> I second that. I use this plugin in "normal" ImageJ, 64bit-Windows.
> Stitching 200 MB 3D stacks together is not a problem. I didn't have a
> case where it wouldn't work if the edges to be stiched where marked as
> ROI. In many cases it also works without ROIs but for stacks it then
> takes noticeably longer and needs more RAM.
>
> The only drawback is that the stiching-plugin is not compatible with
> newer versions of the LOCI Bioformatimporters, i.e. if both are
> installed LOCI doesn't work while stitching does. (so you have to get
> the stitching folder out of your plugins folder and restart ImageJ to
> bioimport.)
>

If you use Fiji instead of naked imageJ
it is much more likely to work,
as thats the context it is developed and tested in.

Before stuff goes into the Fiji updater,
it gets tested by the developers agains the currently bundled versions of
imageJ(A), bio-formats, etc.

If you have a reason to use naked ImageJ instead of Fiji,
we would sure like to hear about it!!!
There should ber nothing that you can do in naked imageJ that cant be done as well or better in Fiji.
(Remember -----  Fiji is just imageJ - batteries included ---- its not a real fork or alternative software, its the same thing with nice stuff added.)

Just let us know what the issue is and we can work towards resolving it.
Fiji has many usability advantages over naked imageJ,
which you should find useful.

If not, please tell us why.

cheers

Dan

> Steffen
>
> --
> ------------------------------------------------------------
> Steffen Dietzel, PD Dr. rer. nat
> Ludwig-Maximilians-Universität München
> Walter-Brendel-Zentrum für experimentelle Medizin (WBex)
> Head of light microscopy
>
> Mail room:
> Marchioninistr. 15, D-81377 München
>
> Building location:
> Marchioninistr. 27,  München-Großhadern

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 )