Finding Shortest Distance from each Particle to a Line

[Mary Cole]

Hello,

    I previously posted about finding a way to outline a number of holes in a cross-section of bone. I have found a way to do this, but now I want to see how far away each hole is from the marrow cavity in the center of the bone.

On ROI manager, I have a list of all of the holes in the bone. I have attached an image of these ROI overlayed on the bone image as a yellow outline (I have removed the particle labels to make it easier to see).



I would like to find a way to measure the shortest distance between each yellow outline and the marrow cavity (white space) in the center of the image. I have also used the magic wand to select the marrow cavity and draw a yellow line.

Is there a plugin that will produce a list of the shortest distance between each ROI and the marrow cavity line?

I can easily make the image into a binary image containing only each ROI and the line surrounding the marrow cavity if that is necessary. I just left the ROI overlayed on the bone to make it easier to visualize.

Thank you very much for your help!

                                                 Sincerely,
                                                 Mary Cole

[John Dunsmuir]

Mary,
One way to proceed is to use Process->Binary->DistanceMap on the binary image of the marrow cavity so that the area outside the cavity is distance mapped.  This will provide an image where the pixel values represent the shortest distance to the cavity.  Applying the roi definitions for the holes from the manager to the distance map and  measuring the minimum value inside each roi will give an estimate of the shortest distance from the hole to the marrow.  You may need to use Analyze Particles on the holes to create a list for the roi manager.  It's a bit fussy but it should work, I haven't tried it yet. Just a thought.
John D.

Mary Cole wrote

Hello,

    I previously posted about finding a way to outline a number of holes in a cross-section of bone. I have found a way to do this, but now I want to see how far away each hole is from the marrow cavity in the center of the bone.

On ROI manager, I have a list of all of the holes in the bone. I have attached an image of these ROI overlayed on the bone image as a yellow outline (I have removed the particle labels to make it easier to see).



I would like to find a way to measure the shortest distance between each yellow outline and the marrow cavity (white space) in the center of the image. I have also used the magic wand to select the marrow cavity and draw a yellow line.

Is there a plugin that will produce a list of the shortest distance between each ROI and the marrow cavity line?

I can easily make the image into a binary image containing only each ROI and the line surrounding the marrow cavity if that is necessary. I just left the ROI overlayed on the bone to make it easier to visualize.

Thank you very much for your help!

                                                 Sincerely,
                                                 Mary Cole

[Michael Schmid]

Hi John, Mary,

yes, I agree that the Distance Map is the best way to measure the distance from the large cavity to the holes.

One minor point that may get overlooked:  As your image looks fairly large and you may have distances larger than 255 pixels, use Process>Binary>Options to set the EDM (=Euclidian Distance Map) output to 16-bit or 32 bit.

If your original image is thresholded to show the holes, you can also use the 'Redirect' feature of 'Set Measurements':  Have the image with the thresholded (small) holes in the foreground and run 'Analyze Particles', but redirect the measurements (in this case, of minimum value) to the image with the distance map.

Michael
________________________________________________________________
On Jul 23, 2013, at 03:18, John Dunsmuir wrote:

> Mary,
> One way to proceed is to use Process->Binary->DistanceMap on the binary
> image of the marrow cavity so that the area outside the cavity is distance
> mapped.  This will provide an image where the pixel values represent the
> shortest distance to the cavity.  Applying the roi definitions for the holes
> from the manager to the distance map and  measuring the minimum value inside
> each roi will give an estimate of the shortest distance from the hole to the
> marrow.  You may need to use Analyze Particles on the holes to create a list
> for the roi manager.  It's a bit fussy but it should work, I haven't tried
> it yet. Just a thought.
> John D.
>
>
> Mary Cole wrote
>> Hello,
>>
>>    I previously posted about finding a way to outline a number of holes
>> in a cross-section of bone. I have found a way to do this, but now I want
>> to see how far away each hole is from the marrow cavity in the center of
>> the bone.
>>
>> On ROI manager, I have a list of all of the holes in the bone. I have
>> attached an image of these ROI overlayed on the bone image as a yellow
>> outline (I have removed the particle labels to make it easier to see).
> <http://imagej.1557.x6.nabble.com/file/n5004083/Image_With_ROI_Flattened.jpg>
>>
>> I would like to find a way to measure the shortest distance between each
>> yellow outline and the marrow cavity (white space) in the center of the
>> image. I have also used the magic wand to select the marrow cavity and
>> draw a yellow line.
>>
>> Is there a plugin that will produce a list of the shortest distance
>> between each ROI and the marrow cavity line?
>>
>> I can easily make the image into a binary image containing only each ROI
>> and the line surrounding the marrow cavity if that is necessary. I just
>> left the ROI overlayed on the bone to make it easier to visualize.
>>
>> Thank you very much for your help!
>>
>>                                                 Sincerely,
>>                                                 Mary Cole
>
>
>
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.com/Finding-Shortest-Distance-from-each-Particle-to-a-Line-tp5004083p5004084.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
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