montage software

[Martin Wessendorf-2]

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Dear all--

I'm imaging some large structures--whole cross-sections of rat
brains--and need to create an image of the entire section by montaging
together a number of images (--16 or so) taken of it's various parts. 
My recollection is that there was once an ImageJ plugin that did that
semi-automatically.  However, I can't find that plugin.  Does anyone
know which one that is?  Alternatively, does anyone know of a better way
to accomplish this than by splicing them all together in PhotoShop?  I
have a number of these to do.

Thanks!

Martin Wessendorf

--
Martin Wessendorf, Ph.D.                   office: [phone]
Assoc Prof, Dept Neuroscience                 lab: [phone]
University of Minnesota             Preferred FAX: [phone]
6-145 Jackson Hall, 321 Church St. SE    Dept Fax: [phone]
Minneapolis, MN  55455                    e-mail: [hidden email]

[Thomas Pengo]

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Hi Martin

the https://imagej.net/Image_Stitching page has a lot of detail and can be
a head-start.

And feel free to reach out and I'd be happy to help!

Cheers
Thomas



________________________________________

Dr. Thomas Pengo
Imaging Informatics Manager
University of Minnesota Informatics Institute
University of Minnesota, Twin Cities Campus
Cancer and Cardiovascular Research Building
2231 6th St SE
Minneapolis, MN 55455



On Thu, Jun 21, 2018 at 10:18 AM, Martin Wessendorf <[hidden email]> wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> Post images on http://www.imgur.com and include the link in your posting.
> *****
>
> Dear all--
>
> I'm imaging some large structures--whole cross-sections of rat brains--and
> need to create an image of the entire section by montaging together a
> number of images (--16 or so) taken of it's various parts.  My recollection
> is that there was once an ImageJ plugin that did that semi-automatically.
> However, I can't find that plugin.  Does anyone know which one that is?
> Alternatively, does anyone know of a better way to accomplish this than by
> splicing them all together in PhotoShop?  I have a number of these to do.
>
> Thanks!
>
> Martin Wessendorf
>
> --
> Martin Wessendorf, Ph.D.                   office: [phone]
> Assoc Prof, Dept Neuroscience                 lab: [phone]
> University of Minnesota             Preferred FAX: [phone]
> 6-145 Jackson Hall, 321 Church St. SE
> <https://maps.google.com/?q=321+Church+St.+SE&entry=gmail&source=g>
> Dept Fax: [phone]
> Minneapolis, MN  55455                    e-mail: [hidden email]
>

[mmodel]

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Dear Martin,

You first arrange images in a stack (Image - Stacks - Images to stack) and the do Image - Stacks - Make Montage

Mike


-----Original Message-----
From: Confocal Microscopy List <[hidden email]> On Behalf Of Martin Wessendorf
Sent: Thursday, June 21, 2018 11:19 AM
To: [hidden email]
Subject: montage software

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Dear all--

I'm imaging some large structures--whole cross-sections of rat brains--and need to create an image of the entire section by montaging together a number of images (--16 or so) taken of it's various parts. My recollection is that there was once an ImageJ plugin that did that semi-automatically.  However, I can't find that plugin.  Does anyone know which one that is?  Alternatively, does anyone know of a better way to accomplish this than by splicing them all together in PhotoShop?  I have a number of these to do.

Thanks!

Martin Wessendorf

--
Martin Wessendorf, Ph.D.                   office: [phone]
Assoc Prof, Dept Neuroscience                 lab: [phone]
University of Minnesota             Preferred FAX: [phone]
6-145 Jackson Hall, 321 Church St. SE    Dept Fax: [phone]
Minneapolis, MN  55455                    e-mail: [hidden email]

[Weis, Michael-2]

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Dear Martin,

I do quite a bit of montaging of TEM, SEM and LM images, the program I use is free and was developed by Microsoft Research division of Microsoft. It is called "Image Composite Editor". I think you will be very happy with it.

Cheers, Michael

Michael Weis
Supervisor,                                             Superviser,
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-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Martin Wessendorf
Sent: June-21-18 8:19 AM
To: [hidden email]
Subject: montage software

*****
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*****

Dear all--

I'm imaging some large structures--whole cross-sections of rat
brains--and need to create an image of the entire section by montaging
together a number of images (--16 or so) taken of it's various parts. 
My recollection is that there was once an ImageJ plugin that did that
semi-automatically.  However, I can't find that plugin.  Does anyone
know which one that is?  Alternatively, does anyone know of a better way
to accomplish this than by splicing them all together in PhotoShop?  I
have a number of these to do.

Thanks!

Martin Wessendorf

--
Martin Wessendorf, Ph.D.                   office: [phone]
Assoc Prof, Dept Neuroscience                 lab: [phone]
University of Minnesota             Preferred FAX: [phone]
6-145 Jackson Hall, 321 Church St. SE    Dept Fax: [phone]
Minneapolis, MN  55455                    e-mail: [hidden email]

[Guy Hagen]

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Dear Martin:
I have had good luck with 'Image Composite Editor' - a free program from
Microsoft.
https://www.microsoft.com/en-us/research/product/computational-photography-applications/image-composite-editor/

cheers,
Guy Hagen

On Thu, Jun 21, 2018 at 9:18 AM, Martin Wessendorf <[hidden email]> wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> Post images on http://www.imgur.com and include the link in your posting.
> *****
>
> Dear all--
>
> I'm imaging some large structures--whole cross-sections of rat brains--and
> need to create an image of the entire section by montaging together a
> number of images (--16 or so) taken of it's various parts.  My recollection
> is that there was once an ImageJ plugin that did that semi-automatically.
> However, I can't find that plugin.  Does anyone know which one that is?
> Alternatively, does anyone know of a better way to accomplish this than by
> splicing them all together in PhotoShop?  I have a number of these to do.
>
> Thanks!
>
> Martin Wessendorf
>
> --
> Martin Wessendorf, Ph.D.                   office: [phone]
> Assoc Prof, Dept Neuroscience                 lab: [phone]
> University of Minnesota             Preferred FAX: [phone]
> 6-145 Jackson Hall, 321 Church St. SE    Dept Fax: [phone]
> Minneapolis, MN  55455                    e-mail: [hidden email]
>

[Martin Wessendorf-2]

*****
To join, leave or search the confocal microscopy listserv, go to:
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Post images on http://www.imgur.com and include the link in your posting.
*****

Thanks to those who responded!  --The word that I needed was
"stitching"--that should let me do what I need. (The built-in montage
function isn't enough for me, since the images overlap.)

Again, thanks!

Martin




On 6/21/2018 10:30 AM, Thomas Pengo wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> Post images on http://www.imgur.com and include the link in your posting.
> *****
>
> Hi Martin
>
> the https://imagej.net/Image_Stitching page has a lot of detail and can be
> a head-start.
>
> And feel free to reach out and I'd be happy to help!
>
> Cheers
> Thomas
>
>
>
> ________________________________________
>
> Dr. Thomas Pengo
> Imaging Informatics Manager
> University of Minnesota Informatics Institute
> University of Minnesota, Twin Cities Campus
> Cancer and Cardiovascular Research Building
> 2231 6th St SE
> Minneapolis, MN 55455
>
>
>
> On Thu, Jun 21, 2018 at 10:18 AM, Martin Wessendorf <[hidden email]> wrote:
>
>> *****
>> To join, leave or search the confocal microscopy listserv, go to:
>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
>> Post images on http://www.imgur.com and include the link in your posting.
>> *****
>>
>> Dear all--
>>
>> I'm imaging some large structures--whole cross-sections of rat brains--and
>> need to create an image of the entire section by montaging together a
>> number of images (--16 or so) taken of it's various parts.  My recollection
>> is that there was once an ImageJ plugin that did that semi-automatically.
>> However, I can't find that plugin.  Does anyone know which one that is?
>> Alternatively, does anyone know of a better way to accomplish this than by
>> splicing them all together in PhotoShop?  I have a number of these to do.
>>
>> Thanks!
>>
>> Martin Wessendorf
>>
>> --
>> Martin Wessendorf, Ph.D.                   office: [phone]
>> Assoc Prof, Dept Neuroscience                 lab: [phone]
>> University of Minnesota             Preferred FAX: [phone]
>> 6-145 Jackson Hall, 321 Church St. SE
>> <https://maps.google.com/?q=321+Church+St.+SE&entry=gmail&source=g>
>> Dept Fax: [phone]
>> Minneapolis, MN  55455                    e-mail: [hidden email]
>>

--
Martin Wessendorf, Ph.D.                   office: [phone]
Assoc Prof, Dept Neuroscience                 lab: [phone]
University of Minnesota             Preferred FAX: [phone]
6-145 Jackson Hall, 321 Church St. SE    Dept Fax: [phone]
Minneapolis, MN  55455                    e-mail: [hidden email]

[Dalton Leprich]

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Dear Martin,

The Nikon Elements software (available at the UIC @ UMN) has a very user
friendly montage creator. I just did multiple of these.

Good luck,

Dalton Leprich

On Thu, Jun 21, 2018 at 12:16 PM, Guy Hagen <[hidden email]> wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> Post images on http://www.imgur.com and include the link in your posting.
> *****
>
> Dear Martin:
> I have had good luck with 'Image Composite Editor' - a free program from
> Microsoft.
> https://www.microsoft.com/en-us/research/product/
> computational-photography-applications/image-composite-editor/
>
> cheers,
> Guy Hagen
>
> On Thu, Jun 21, 2018 at 9:18 AM, Martin Wessendorf <[hidden email]>
> wrote:
>
> > *****
> > To join, leave or search the confocal microscopy listserv, go to:
> > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> > Post images on http://www.imgur.com and include the link in your
> posting.
> > *****
> >
> > Dear all--
> >
> > I'm imaging some large structures--whole cross-sections of rat
> brains--and
> > need to create an image of the entire section by montaging together a
> > number of images (--16 or so) taken of it's various parts.  My
> recollection
> > is that there was once an ImageJ plugin that did that semi-automatically.
> > However, I can't find that plugin.  Does anyone know which one that is?
> > Alternatively, does anyone know of a better way to accomplish this than
> by
> > splicing them all together in PhotoShop?  I have a number of these to do.
> >
> > Thanks!
> >
> > Martin Wessendorf
> >
> > --
> > Martin Wessendorf, Ph.D.                   office: [phone]
> > Assoc Prof, Dept Neuroscience                 lab: [phone]
> > University of Minnesota             Preferred FAX: [phone]
> > 6-145 Jackson Hall, 321 Church St. SE    Dept Fax: [phone]
> > Minneapolis, MN  55455                    e-mail: [hidden email]
> >
>

--
Dalton J. Leprich
PhD Student, Geobiology
University of Minnesota, Earth Science
[hidden email]

[S. Pagakis (IIBEAA)]

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Dear Martin

in the past we have used

http://bigwww.epfl.ch/thevenaz/turboreg/ <http://bigwww.epfl.ch/thevenaz/turboreg/>
and
http://bigwww.epfl.ch/thevenaz/mosaicj/ <http://bigwww.epfl.ch/thevenaz/mosaicj/>

but the distribution is since 2011 and I do not now whether they still work.  If you try them, I would be interested to find out if they still do

Stamatis

> On 21 Jun, 2018, at 18:18, Martin Wessendorf <[hidden email]> wrote:
>
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> Post images on http://www.imgur.com and include the link in your posting.
> *****
>
> Dear all--
>
> I'm imaging some large structures--whole cross-sections of rat brains--and need to create an image of the entire section by montaging together a number of images (--16 or so) taken of it's various parts.  My recollection is that there was once an ImageJ plugin that did that semi-automatically.  However, I can't find that plugin.  Does anyone know which one that is?  Alternatively, does anyone know of a better way to accomplish this than by splicing them all together in PhotoShop?  I have a number of these to do.
>
> Thanks!
>
> Martin Wessendorf
>
> --
> Martin Wessendorf, Ph.D.                   office: [phone]
> Assoc Prof, Dept Neuroscience                 lab: [phone]
> University of Minnesota             Preferred FAX: [phone]
> 6-145 Jackson Hall, 321 Church St. SE    Dept Fax: [phone]
> Minneapolis, MN  55455                    e-mail: [hidden email]

******************************
Stamatis Pagakis Ph.D.
Senior Research Scientist
Head, Biological Imaging
Biomedical Research Foundation, Academy of Athens
Soranou Efessiou 4, Athens 115 27 - Greece
M:     [phone]                
W:     [phone]
FAX: [phone]
http://www.bioacademy.gr/faculty-details/HM4/Stamatis <http://www.bioacademy.gr/Faculty/core.php?cr=17>