Re: Stereology with Image J?

Posted by Jacqueline Ross on Jan 04, 2007; 9:12pm
URL: http://imagej.273.s1.nabble.com/sperm-head-area-tp3700677p3700683.html

Dear All,

Since Martin has mentioned the Grid plugin which works well for
systematic sampling, can anyone remind me how you designate the size of
the grid relative to your image field that you should use for sampling
for manual counting, etc.?

There's also a macro called DrawRandomDots that seems to follow the
Chalkley Grid method and draws 25 random dots on the image. Can anyone
tell me if the dots are programmed to be the correct size for sampling
relative to any image?

Cheers,

Jacqui.

Jacqueline Ross
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.health.auckland.ac.nz/biru/ 

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
Martin Wessendorf
Sent: 05 January 2007 09:32
To: [hidden email]
Subject: Re: Stereology with Image J?

David Finkelstein wrote:

> Are there any Stereology plug ins for Image J.
> Specifically, an ability to drop\superimpose a counting frame (of user
> defined size and step size) onto a section image.  Then the ability to
zoom
> into each of the counting frames in order.

There's the "grid" plugin ("Draw line or point grids":
http://rsb.info.nih.gov/ij/plugins/grid.html).  It's good for randomly
creating a grid over an image, e.g. for cavalieri estimations of volume
or to create a random set of points for systematic random sampling.

For a counting frame, we simply draw one on a piece of acetate that we
tape to the computer monitor.  Very low-tech but it works.

The "IJStage and IJSerial (microscope stage control and serial I/O)"
plugin (http://www.eslide.net/ijstage.php) appears able to control some
types of stages but you'd need to program in the specifics for
systematic random sampling.

Good luck--

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: martinw[at]med.umn.edu