How to make montages in Image J

[Shilpashree Balakrishnan]

Hello,
I have a large section and have to take multiple images of my section under the microscope and then stich them together to do density counting. Could someone tell me how to do montaging using ImageJ ?
thank you,
regards,
Shilpa

[Divya Rathore]

Image >> Stack >> Make Montage...

cheers,
D. Rathore


----- Original Message -----
From: "Shilpashree Balakrishnan" <[hidden email]>
To: <[hidden email]>
Sent: Tuesday, February 06, 2007 5:24 PM
Subject: How to make montages in Image J

> Hello,
> I have a large section and have to take multiple images of my section
> under the microscope and then stich them together to do density counting.
> Could someone tell me how to do montaging using ImageJ ?
> thank you,
> regards,
> Shilpa
>
> __________ NOD32 2042 (20070206) Information __________
>
> This message was checked by NOD32 antivirus system.
> http://www.eset.com
>
>

[Divya Rathore]

wait.. i guess your case is not that simple.. you need to register the
images!

Divya Rathore
www.adislindia.com/people/~divya/index.html


----- Original Message -----
From: "D. Rathore" <[hidden email]>
To: <[hidden email]>
Sent: Wednesday, February 07, 2007 11:01 AM
Subject: Re: How to make montages in Image J

> Image >> Stack >> Make Montage...
>
> cheers,
> D. Rathore
>
>
> ----- Original Message -----
> From: "Shilpashree Balakrishnan" <[hidden email]>
> To: <[hidden email]>
> Sent: Tuesday, February 06, 2007 5:24 PM
> Subject: How to make montages in Image J
>
>
>> Hello,
>> I have a large section and have to take multiple images of my section
>> under the microscope and then stich them together to do density counting.
>> Could someone tell me how to do montaging using ImageJ ?
>> thank you,
>> regards,
>> Shilpa
>>
>> __________ NOD32 2042 (20070206) Information __________
>>
>> This message was checked by NOD32 antivirus system.
>> http://www.eset.com
>>
>>
>
> __________ NOD32 2042 (20070206) Information __________
>
> This message was checked by NOD32 antivirus system.
> http://www.eset.com
>
>

[Albert Cardona]

Hi,

I've created an ImageJ plugin, TrakEM2, to handle lots of images in a
similar way that photoshop would, but with no memory limitations and
fully integrated in ImageJ.
Automatic registration is going to make it in the next release (it's
already working, but not just ready for the non-savvy user). My plugin
is here (and does not require a database, I need to update the website),
in beta version:
http://www.ini.uzh.ch/~acardona/trakem2.html


On the meanwhile, there are a couple of plugins to register images and
to make montages, which will work to a reasonable extent, depending on
your data.

For example:
http://www.cs.uta.fi/~vt72556/software/largemontage/

Also, go to the ImageJ plugin web page and search for "registr", there
are many occurrences.

Alternatively, just use Photoshop's auto montage -just be sure to have
enough RAM and HD swap space to fit them all. Works quite ok, if images
are simple enough (TEM images don't work well, for example).

Albert

[Vincenzo Della Mea]

Try this plugin, which is made exaclty for that: http://www.cs.uta.fi/ 
~vt72556/software/largemontage/
Vincenzo

Il giorno 06/feb/07, alle ore 12:54, Shilpashree Balakrishnan ha  
scritto:

> Hello,
> I have a large section and have to take multiple images of my  
> section under the microscope and then stich them together to do  
> density counting. Could someone tell me how to do montaging using  
> ImageJ ?
> thank you,
> regards,
> Shilpa

* Vincenzo Della Mea
* Medical Informatics, Telemedicine and Ehealth Lab
* University of Udine, Italy
* http://mitel.dimi.uniud.it/  -  http://www.eslide.net

[Gabriel Landini]

On Thursday 08 February 2007 13:00:48 Vincenzo Della Mea wrote:
> Try this plugin, which is made exaclty for that: http://www.cs.uta.fi/
> ~vt72556/software/largemontage/

I think that the plugin expects a fixed overlap size in one of the directions.
This is almost impossible to achieve if the capture was done manually.

I look forward to see whether the new version of TrakEM can align RGB mosaics
with variable overlaps.

Any hints are welcome.
Cheers,

G.

[Albert Cardona]

> I think that the plugin expects a fixed overlap size in one of the directions.
> This is almost impossible to achieve if the capture was done manually.
>
> I look forward to see whether the new version of TrakEM can align RGB mosaics
> with variable overlaps.
>
>  
Yes it can, but at a price: one will need the C library fftw version 2
installed (2.1.3 recommended), and its java jfftw.jar wrapper (both are
GPL). The merging is a few weeks away -still lots of details to polish.
The algorithm is noise-resistant and won't (can't) be perfect, but works
near perfection when information is provided beforehand on the overlap
range  (like, from 0 to 10%), and the tile relative position to other
tiles (as in a grid, to prevent incorrect mismatches).

If you have your images numbered 1,2,3,4,5,6,7,8 and that is 2 rows of 4
images, then all that will be queried for is the estimated overlap range.


albert

[Gabriel Landini]

On Thursday 08 February 2007 19:02:15 Albert Cardona wrote:
> Yes it can, but at a price: one will need the C library fftw version 2
> installed (2.1.3 recommended), and its java jfftw.jar wrapper (both are
> GPL).

I have fftw3 installed (3.1.2-19) would this work?

What about the jfftw.jar? Where does one get that from?
I cannot see in:
http://www.ph.ed.ac.uk/~wjh/teaching/Java/fft/

Cheers,

Gabriel

[dscho]

Hi,

On Fri, 9 Feb 2007, Gabriel Landini wrote:

> On Thursday 08 February 2007 19:02:15 Albert Cardona wrote:
> > Yes it can, but at a price: one will need the C library fftw version 2
> > installed (2.1.3 recommended), and its java jfftw.jar wrapper (both are
> > GPL).
>
> I have fftw3 installed (3.1.2-19) would this work?
>
> What about the jfftw.jar? Where does one get that from?
> I cannot see in:
> http://www.ph.ed.ac.uk/~wjh/teaching/Java/fft/

Maybe this works:

        ftp://ftp.fftw.org/pub/fftw/jfftw-1.2.zip

Hth,
Dscho

[Albert Cardona]

Wait! The registration is neither ready nor released yet with TrakEM2.
The reason to use fftw version 2 is that  the java wrapper fftw.jar is
designed for version 2.

Albert