JACoP

[gauri]

Hello
I am using JACoP for colocalization , but it asks me for xy calibration and z calibration . i am not sure what values do i punch in there. it ask in nm. by default it shows 67nm for xy calibration and 200 for z calibration. i dont know what these values mean. i use confocal SP5 laser microscope and excitation wavelength of 488 and 561. Can somebody tell me what these xy calibration values should be and what do they mean.
Also it there is a column for x shift. what does that mean. i punched in some random numbers but it did not make any difference.

Gauri

[Vergara, Leoncio A.]

If I understood your question, this is very basic knowledge.

xy calibration is asking for the dimension of the pixels in your images. Usually pixels are square. Your confocal software should be able to tell you the pixel size. Pixel size depends on the magnification but is mainly determined by the scanning pattern, number of pixels in x and y and zoom factor.

z calibraton is basically the z-step you used when capturing a z-series (aka z-stack) in your confocal. If you are only capturing single planes, you can probably ignore that dimension.

the x, y and z dimensions determine the size of the voxels in volumetric datasets.

Sorry if I misunderstood this part of your question.

________________________________________
From: ImageJ Interest Group [[hidden email]] On Behalf Of gauri [[hidden email]]
Sent: Wednesday, March 16, 2011 10:27 PM
To: [hidden email]
Subject: JACoP

Hello
I am using JACoP for colocalization , but it asks me for xy calibration and
z calibration . i am not sure what values do i punch in there. it ask in nm.
by default it shows 67nm for xy calibration and 200 for z calibration. i
dont know what these values mean. i use confocal SP5 laser microscope and
excitation wavelength of 488 and 561. Can somebody tell me what these xy
calibration values should be and what do they mean.
Also it there is a column for x shift. what does that mean. i punched in
some random numbers but it did not make any difference.

Gauri

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[Jacqueline Ross]

Hi Gauri,

These values are the voxel/pixel sizes. You get this information from
the calibration data of your microscope.

If you are using data from a Leica TCS SP5, this is supported with the
Bioformats plugin, so you should be able to open your original data
directly and "get" the calibration data from the image.

Click on the "Micro" tab and select "Confocal". Then click "Get
Calibration from Image A" or "Get Calibration from Image B". Of course
this calibration information is extremely important if you are trying to
determine whether two labels are "colocalised/colocated".

The X shift is to do with one of the randomization routines.

You really need to read the documentation associated with this plugin if
you are going to use it.

There are two references that you need to read and understand, which
were written by the authors of the plugin. Both are available as links
from this page:
http://imagejdocu.tudor.lu/doku.php?id=plugin:analysis:jacop_2.0:just_an
other_colocalization_plugin:start listed under References/Citation.

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: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
gauri
Sent: Thursday, 17 March 2011 4:27 p.m.
To: [hidden email]
Subject: JACoP

Hello
I am using JACoP for colocalization , but it asks me for xy calibration
and
z calibration . i am not sure what values do i punch in there. it ask in
nm.
by default it shows 67nm for xy calibration and 200 for z calibration. i
dont know what these values mean. i use confocal SP5 laser microscope
and
excitation wavelength of 488 and 561. Can somebody tell me what these xy
calibration values should be and what do they mean.
Also it there is a column for x shift. what does that mean. i punched in
some random numbers but it did not make any difference.

Gauri

--
View this message in context:
http://imagej.588099.n2.nabble.com/JACoP-tp6179605p6179605.html
Sent from the ImageJ mailing list archive at Nabble.com.