FW: Help for publication

[Brad Wakeman]

Hello,

I'm looking for a way to determine and mark the centre of the rectangle created by using the rectangular selector tool in ImageJ




So that I can use ImageJ to determine the centre of the ring of eye muscles that controls eye movements from patient scans.  I need to be able to make a line connecting the centres and then be able to measure the angles of the eye muscles relative to the centre of the muscle cone.  (like this:)



For a study for publication.  I'm not a programmer and I need help... Anyone able and interested in making make some kind of plug in to automate this process and be included in the publication?  It seems to me that it shouldn't be that difficult for someone familiar with the programming, but it's completely beyond me!

Brad Wakeman BSc, OC(C)
Department of Ophthalmology/Faculty of Medicine & Dentistry
Rm 2319, Royal Alexandra Hospital * 10240 Kingsway Avenue
Edmonton * Alberta * Canada * T5H 3V9
Telephone: [phone] * Fax: [phone]

Pediatric Ophthalmology and Adult Strabismus Clinic

Room 2-133 CSB, University of Alberta Hospital
Edmonton * Alberta * Canada * T6G 2G6
Telephone: [phone] * Fax: [phone]




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[Gabriel Landini]

On Friday 07 Jun 2013 20:41:57 Brad Wakeman wrote:
> I'm looking for a way to determine and mark the centre of the rectangle
> created by using the rectangular selector tool in ImageJ

This might help although it is based on a circle not a square:
ThreePointCircularROI plugin. This plugin creates a circular ROI based on 3
user selected points on an image. The log window reports the coordinates of
the centre of the circle and its radius. Co-linear points (that define an
impossible circle) return a radius of -1.

http://www.dentistry.bham.ac.uk/landinig/software/software.html

Cheers
Gabriel

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[Peter Haub]

Hi Brad,
your application seems to be not to complicated.
The most important aspect is to align the two images (channels).
Otherwise the points selected in one channel can not be related to the
points of the other channel.

Here is an easy way to do this:

1) Images should have the same size.
In case of your example I used [ Image / Adjust / canvas Size ..] to
adjust the size. ( Do not use the Scale function! )

2) Overlay both images as planes in an RGB image with [ Image / Color /
Merge ].

3) Shifted and aligned the panes interactive with the plugin:
Align_RGB_planes (Gabriel Landini).
You can find it on the ImageJ plugin website.


As a starting point for your macro you could simply use:
         getSelectionBounds(x, y, width, height);
         IJ.log("X: "+x +"  Y: "+y +"  W: "+width +"  H: "+height);

It will print the center position of the rectangle and points in the
ImageJ log window. Run it after every selection in the image.

The rest is vector math.

Hope this helps.

Peter


On 07.06.2013 21:41, Brad Wakeman wrote:

> Hello,
>
> I'm looking for a way to determine and mark the centre of the rectangle created by using the rectangular selector tool in ImageJ
>
>
>
>
> So that I can use ImageJ to determine the centre of the ring of eye muscles that controls eye movements from patient scans.  I need to be able to make a line connecting the centres and then be able to measure the angles of the eye muscles relative to the centre of the muscle cone.  (like this:)
>
>
>
> For a study for publication.  I'm not a programmer and I need help... Anyone able and interested in making make some kind of plug in to automate this process and be included in the publication?  It seems to me that it shouldn't be that difficult for someone familiar with the programming, but it's completely beyond me!
>
> Brad Wakeman BSc, OC(C)
> Department of Ophthalmology/Faculty of Medicine & Dentistry
> Rm 2319, Royal Alexandra Hospital * 10240 Kingsway Avenue
> Edmonton * Alberta * Canada * T5H 3V9
> Telephone: [phone] * Fax: [phone]
>
> Pediatric Ophthalmology and Adult Strabismus Clinic
>
> Room 2-133 CSB, University of Alberta Hospital
> Edmonton * Alberta * Canada * T6G 2G6
> Telephone: [phone] * Fax: [phone]
>
>
>
>
>    ________________________________
> This message and any attached documents are only for the use of the intended recipient(s), are confidential and may contain privileged information. Any unauthorized review, use, retransmission, or other disclosure is strictly prohibited. If you have received this message in error, please notify the sender immediately, and then delete the original message. Thank you.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

... [show rest of quote]

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