question about imagej

[Carlos Lizama]

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
*****

hi,

Im working with imagej. but i have a problem. All the time when I acquired the
photos from library (.lif) the leica confocal scope, the quality of the image is
completly different the original observed in the leica scope. Somebody know
How Can I set up imageJ to get the same quality?  


thanks carlos

[mmodel]

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
*****

Hi Carlos, How do you know that the quality of images is different? Have you compared pixel intensities? It could be that the default display is different, not the image itself. (It has been a long time since I worked with Leica files but I suppose that the LOCI plugin should open files without any distortion)

Mike Model

________________________________________
From: Confocal Microscopy List [[hidden email]] On Behalf Of Carlos Lizama [[hidden email]]
Sent: Monday, May 28, 2012 3:47 PM
To: [hidden email]
Subject: question about imagej

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
*****

hi,

Im working with imagej. but i have a problem. All the time when I acquired the
photos from library (.lif) the leica confocal scope, the quality of the image is
completly different the original observed in the leica scope. Somebody know
How Can I set up imageJ to get the same quality?


thanks carlos

[Jacqueline Ross]

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
*****

Hi Carlos,

Check whether or not you have the image being scaled.

You can look at "Edit - Options - Conversion Options". Turn off "Scale when Converting".

Also, if you are using Bioformats to open the files, then make sure "Autoscale" is turned off in the Bioformats Import Options under Color.

Hopefully, this will help.

If it still looks different, it might be that your monitor is very different from the one on the scope.

Kind regards,

Jacqui

Jacqueline Ross

Biomedical Imaging Microscopist
Biomedical Imaging Research Unit
School of Medical Sciences
Faculty of Medical & Health Sciences
The University of Auckland
Private Bag 92019
Auckland, NEW ZEALAND

Tel: [phone] Ext 87438
Fax: [phone]

http://www.fmhs.auckland.ac.nz/sms/biru/

-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Carlos Lizama
Sent: Tuesday, 29 May 2012 7:48 a.m.
To: [hidden email]
Subject: question about imagej

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
*****

hi,

Im working with imagej. but i have a problem. All the time when I acquired the
photos from library (.lif) the leica confocal scope, the quality of the image is
completly different the original observed in the leica scope. Somebody know
How Can I set up imageJ to get the same quality?  


thanks carlos

[Turnbull, Lon]

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
*****

Hi,

When using imageJ with three channel acquisition images contrast stretching is performed.  When examining images in which one of the channels can be very weak for some samples and not for other samples it is much easier to see the difference between the samples, if there were no contrast stretching.

Is it possible to turn off the automatic contrast stretching?

Lon


-----------------------------------------------------------------

Lon Turnbull, Ph.D.
Microscope Supervisor
Department of Biological Sciences
University of North Texas
940-369-8721
[hidden email]

[mmodel]

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
*****

I think ImageJ automatically sets contrast based on the first image of a stack and then applies the same limits to the rest of the stack. You can always change the display manually (Image-adjust-brightness/contrast-"reset" or "auto" or enter numbers), but if there is a big difference between images within a stack then some will always be either too bright or too dark

-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Turnbull, Lon
Sent: Tuesday, May 29, 2012 4:35 PM
To: [hidden email]
Subject: Another question about imageJ

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
*****

Hi,

When using imageJ with three channel acquisition images contrast stretching is performed.  When examining images in which one of the channels can be very weak for some samples and not for other samples it is much easier to see the difference between the samples, if there were no contrast stretching.

Is it possible to turn off the automatic contrast stretching?

Lon


-----------------------------------------------------------------

Lon Turnbull, Ph.D.
Microscope Supervisor
Department of Biological Sciences
University of North Texas
940-369-8721
[hidden email]

[Jacqueline Ross]

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
*****

Hi Lon,

The email that I sent in response to Carlos a couple of days ago should answer your question.

Check whether or not you have the image being scaled.

You can look at "Edit - Options - Conversion Options". Turn off "Scale when Converting".

Also, if you are using Bioformats to open the files, then make sure "Autoscale" is turned off in the Bioformats Import Options under Color.

You may want to address further questions about ImageJ to the ImageJ listserver: http://rsbweb.nih.gov/ij/list.html

Kind regards,

Jacqui


Jacqueline Ross

Biomedical Imaging Microscopist
Biomedical Imaging Research Unit
School of Medical Sciences
Faculty of Medical & Health Sciences
The University of Auckland
Private Bag 92019
Auckland, NEW ZEALAND

Tel: [phone] Ext 87438
Fax: [phone]

http://www.fmhs.auckland.ac.nz/sms/biru/

-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of MODEL, MICHAEL
Sent: Wednesday, 30 May 2012 9:10 a.m.
To: [hidden email]
Subject: Re: Another question about imageJ

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
*****

I think ImageJ automatically sets contrast based on the first image of a stack and then applies the same limits to the rest of the stack. You can always change the display manually (Image-adjust-brightness/contrast-"reset" or "auto" or enter numbers), but if there is a big difference between images within a stack then some will always be either too bright or too dark

-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Turnbull, Lon
Sent: Tuesday, May 29, 2012 4:35 PM
To: [hidden email]
Subject: Another question about imageJ

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
*****

Hi,

When using imageJ with three channel acquisition images contrast stretching is performed.  When examining images in which one of the channels can be very weak for some samples and not for other samples it is much easier to see the difference between the samples, if there were no contrast stretching.

Is it possible to turn off the automatic contrast stretching?

Lon


-----------------------------------------------------------------

Lon Turnbull, Ph.D.
Microscope Supervisor
Department of Biological Sciences
University of North Texas
940-369-8721
[hidden email]