Basic Help

[bridesnz]

Hi everyone, I am after some basic advice on how ImageJ works.
I am analysing fish movement by utilizing a manual tracking plugin. I am wondering what exactly the x and y coordinates refer to as well as the distance and pixel column. Any help would be great!
Thanking you all!

[Robert Baer]

Hi everyone, I am after some basic advice on how ImageJ works.
I am analysing fish movement by utilizing a manual tracking plugin. I am
wondering what exactly the x and y coordinates refer to as well as the
distance and pixel column. Any help would be great!
Thanking you all!
-----------------------------------------
These would seem quite basic questions and suggest that you need to do a
little reading early on.  I would suggest that you look at the documentation
available at the ImageJ site and through the help menu.

An image is made of small squares (not really but start with that vision)
called pixels arranged on an x - y grid.  The y tells you how many pixels
down from the top of your image your mouse is.  The x tells you how many
pixels up from the bottom you mouse is.  The value is the "blackness" or
"whiteness" or "grayness" of the image where your mouse is.  Usually, 0 for
black and 255 for white, but sometimes the other way around depending on the
convention being used.  Gray is in between.  When you draw a line with the
line tool, the length is the length in pixels and angle is the angle above
horizontal on the standard unit circle of the line.

If you are analyzing fish, you pictures may have "real world units"
associated with your work.  for example you may be able to tell exactly how
many pixels is an inch if there is a ruler beside your fish.  You can then
use the Analyze | Set Scale dialog box to make many of the above units
appear in inches or mm or cm or feet or what ever is appropriate.  You must
calibrate each image or a pixel is just a pixel.  Hope this gets you
started, but again I urge you to read the great documentation on the web
site or wiki.

Rob



------------------------------------------
Robert W. Baer, Ph.D.
Professor of Physiology
Kirksville College of Osteopathic Medicine
A. T. Still University of Health Sciences
800 W. Jefferson St.
Kirksville, MO 63501
660-626-2322
FAX [phone]

_______________________________________________________

ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[bridesnz]

Thank you Rob,

I have found some extremely useful sources of information. However, I am still a little unsure about the process. In particular I am not sure what to enter into the x/y calibration box. For what I am measuring, I have set the scale at 1mm=2.5 pixels, does this mean I put 1 in the x/y calibration box?

Thanking you,

[bridesnz]

ok

---

Date: Tue, 29 May 2012 17:31:17 -0700
From: [hidden email]
To: [hidden email]
Subject: Re: Basic Help

Thank you Rob,

I have found some extremely useful sources of information. However, I am still a little unsure about the process. In particular I am not sure what to enter into the x/y calibration box. For what I am measuring, I have set the scale at 1mm=2.5 pixels, does this mean I put 1 in the x/y calibration box?

Thanking you,

---

If you reply to this email, your message will be added to the discussion below:

http://imagej.1557.n6.nabble.com/Basic-Help-tp4998825p4998845.html

To unsubscribe from Basic Help, click here.
NAML

[Glen MacDonald-2]

2.5 = pixels/mm 1/2.5 = mm/pixel
for your example 1 mm = 2.5 pixels, then 1/2.5 = .4 mm/pixel in the Properties, enter 0.4 for size and mm for units, (or 400 for size and microns for units).  

http://imagej.nih.gov/ij/docs/guide/userguide-25.html#toc-Subsection-25.4
Open Image>Properties, enter the known pixel size and the units, optionally clicking on 'global will set scale on all open images.

With an image of a stage micrometer, or other standard of known dimensions,
measure a length with the straight line tool (Analyze>Set Measurements>Perimeter) then Analyze>Measure
Open the Analyze>Set Scale dialog
http://imagej.nih.gov/ij/docs/guide/userguide-27.html#toc-Subsection-27.8
your measurement will be present as distance in pixels, type in the known distance and enter unit of length
the new scale will update in Image>Properties

Glen
Glen MacDonald
Core for Communication Research
Virginia Merrill Bloedel Hearing Research Center
Box 357923
University of Washington
Seattle, WA 98195-7923  USA
[phone]
[hidden email]








On May 29, 2012, at 5:31 PM, bridesnz wrote:

> Thank you Rob,
>
> I have found some extremely useful sources of information. However, I am
> still a little unsure about the process. In particular I am not sure what to
> enter into the x/y calibration box. For what I am measuring, I have set the
> scale at 1mm=2.5 pixels, does this mean I put 1 in the x/y calibration box?
>
> Thanking you,
>
> --
> View this message in context: http://imagej.1557.n6.nabble.com/Basic-Help-tp4998825p4998845.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> _______________________________________________________
>
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

_______________________________________________________

ImageJ mailing list: http://imagej.nih.gov/ij/list.html