Using Find Edge Function

[AMD123]

Hello,

How can I define ROI on boundaries of an object when it is not a composite ROI?

I want the RIO to be the area inscribed in my object; so I used " find edge" and the edges were perfectly defined, but when I try to "create selection"  I get this message " This command creates a composite selection from a mask ( 8-bit binary image with white background) or from an image that has been thresholded..."

Thank you.

[Peter Haub]

Hello AMD123,

'Find Edges' uses as 3x3 Sobel filter for edge detection. The function
does not create ROIs.

To create a ROI on the image (either the original image or the 'edge
image') you can use the WAND tracing tool.

-Select the wand tool and click onto the edge in your image
- Don't forget to adjust the tolerance by right clicking onto the tool icon
(Alternatively you can threshold the image, use 'Process/Binary/Make
Binary' or use 'Process/Binary/Create Mask' after 'Find Edges' before
using the wand tool. In this case you can use the wand tool with zero
tolerance.)

You can also try to select your object with the wand tool without edge
filtering by directly clicking into the object area. There will be a
good chance that this will work presuming limited object intensity
variations, distinct disparity between object and background intensity
and appropriate tolerance setting.

Best regards,

Peter

On 27.11.2015 22:53, AMD123 wrote:

> Hello,
>
> How can I define ROI on boundaries of an object when it is not a composite
> ROI?
>
> I want the RIO to be the area inscribed in my object; so I used " find edge"
> and the edges were perfectly defined, but when I try to "create selection"
> I get this message " This command creates a composite selection from a mask
> ( 8-bit binary image with white background) or from an image that has been
> thresholded..."
>
> Thank you.
>
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.com/Using-Find-Edge-Function-tp5015040.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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[Michael Schmid]

Hi Anonymous,

as I understand it, you can't get the object with Image>Adjust>Threshold,
but you see a closed outline with 'Find Edges'.

Withour 'Find Edges' there are several possibilities to preprocess before
Thresholding:
 - Remove the background, e.g. Process>Subtract Background
 - Apply an edge-preserving blur, e.g. the Thresholded Blur [1]

You can also run 'Find Edges', threshold the outline, and then use
'Analyze Particles' (on the areas including the inner holes). Or apply the
threshold and run 'Fill Holes' and then shrink it by half the width of the
outline (Process>Filters>Minimum), to get an area that is closer to the
original size.

Without 'Find Edges', you can also try the gradient threshold of the
Versatile Wand [2] (possibly after some [edge-preserving] smoothing).

If you are using Fiji, the Trainable Weka Segmentation might also help.

Without seeing the image, one can't say what is the best way...

Michael

[1]
http://imagejdocu.tudor.lu/doku.php?id=plugin:filter:thresholded_blur:start
[2]
http://imagejdocu.tudor.lu/doku.php?id=plugin:segmentation:versatile_wand:start
_____________________________

On Fri, November 27, 2015 22:53, AMD123 wrote:

> Hello,
>
> How can I define ROI on boundaries of an object when it is not a composite
> ROI?
>
> I want the RIO to be the area inscribed in my object; so I used " find
> edge"
> and the edges were perfectly defined, but when I try to "create selection"
> I get this message " This command creates a composite selection from a
> mask
> ( 8-bit binary image with white background) or from an image that has been
> thresholded..."
>
> Thank you.

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