Convert blobs/points to equal size circles

[roymf]

I have a binary image with some spots/blobs/points as shown below. I would like to convert them all to circles of the same size. The diameter doesn't matter so much. I tried using 'Erode' followed by 'Ultimate point' to make each point a pixel. Then use 'Dilate' to bring up the size but that produces a square. If anyone has any suggestions, please let me know. Thanks, Roy

[Jason Miller]

Hi Roy-

I recently learned that some of the shape artifacts that arise when using
dilate and erode in ImageJ can be eliminated by using the dilate and erode
functions built into the BioVoxxel plugin. Jan Brocher, developer of
BioVoxxel, talked about this at the recent ImageJ conference in Madison:

http://fiji.sc/BioVoxxel_Toolbox#EDM_Binary_Operations

Best
-Jason

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University of Michigan Kellogg Eye Center


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On Fri, Sep 25, 2015 at 12:52 PM, roymf <[hidden email]> wrote:

> I have a binary image with some spots/blobs/points as shown below. I would
> like to convert them all to circles of the same size. The diameter doesn't
> matter so much. I tried using 'Erode' followed by 'Ultimate point' to make
> each point a pixel. Then use 'Dilate' to bring up the size but that
> produces
> a square. If anyone has any suggestions, please let me know.Thanks,Roy
> <http://imagej.1557.x6.nabble.com/file/n5014466/new1.jpg>
>
>
>
> --
> View this message in context:
> http://imagej.1557.x6.nabble.com/Convert-blobs-points-to-equal-size-circles-tp5014466.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 Roi,

for a dilation operation with circular mask, you can use Process>Filters>Maximum if your spots have a pixel value of 255 on background 0, or Process>Filters>Minimum, if the spots are 0 on background 255.

Michael
________________________________________________________________
On Sep 25, 2015, at 18:52, roymf wrote:

> I have a binary image with some spots/blobs/points as shown below. I would
> like to convert them all to circles of the same size. The diameter doesn't
> matter so much. I tried using 'Erode' followed by 'Ultimate point' to make
> each point a pixel. Then use 'Dilate' to bring up the size but that produces
> a square. If anyone has any suggestions, please let me know.Thanks,Roy
> <http://imagej.1557.x6.nabble.com/file/n5014466/new1.jpg>
>
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.com/Convert-blobs-points-to-equal-size-circles-tp5014466.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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[gankaku]

Hi all,

thanks Jason, for quoting.
Indeed the EDM Binary operatiosn should do the job.
The Maximum... function also gives you circles but thouse will be in
different intensities and you will need to threshold tehm afterwards in
addition.
The other option would be analyze particles, take x and y coordinates and
create circular selections if you would need the circles as ROIs, because
thouse you could add to the ROI Manager.

regards,
Jan

2015-09-25 19:27 GMT+02:00 Michael Schmid <[hidden email]>:

> Hi Roi,
>
> for a dilation operation with circular mask, you can use
> Process>Filters>Maximum if your spots have a pixel value of 255 on
> background 0, or Process>Filters>Minimum, if the spots are 0 on background
> 255.
>
> Michael
> ________________________________________________________________
> On Sep 25, 2015, at 18:52, roymf wrote:
>
> > I have a binary image with some spots/blobs/points as shown below. I
> would
> > like to convert them all to circles of the same size. The diameter
> doesn't
> > matter so much. I tried using 'Erode' followed by 'Ultimate point' to
> make
> > each point a pixel. Then use 'Dilate' to bring up the size but that
> produces
> > a square. If anyone has any suggestions, please let me know.Thanks,Roy
> > <http://imagej.1557.x6.nabble.com/file/n5014466/new1.jpg>
> >
> >
> >
> > --
> > View this message in context:
> http://imagej.1557.x6.nabble.com/Convert-blobs-points-to-equal-size-circles-tp5014466.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
>

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[roymf]

Hi all. Thanks for your replies. The EDM Binary Operations from Biovoxxel along with maximum produces a much better result already. Thanks, Roy.