Water-shedding non-circular objects (w/ Attachment)

[Clay Morton]

 Hey good people, I was wondering if anyone knew of a way to successfully separate touching particles that are not circular is shape. It seems that the water-shedding function only separates touching particles if they are circular, but has difficulty in correctly separating different shapes. Attached is an image that I have been working with. As you can see when a "crescent" shaped cell (sickle cell) is touching a circular cell (flat red blood cell), proper division does not occur. Also elliptical cells are sometimes cut in half (lower middle image).?Any ideas how I could correct this?

Thanks



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[Niko Ehrenfeuchter]

Dear anonymous,

you could have a look at Jan Brocher's "Irregular Watershed":

http://fiji.sc/BioVoxxel_Toolbox#Watershed_Irregular_Structures

Cheers
Niko

On 19.03.2015 22:36, Clay Morton wrote:
>   Hey good people, I was wondering if anyone knew of a way to successfully separate touching particles that are not circular is shape. It seems that the water-shedding function only separates touching particles if they are circular, but has difficulty in correctly separating different shapes. Attached is an image that I have been working with. As you can see when a "crescent" shaped cell (sickle cell) is touching a circular cell (flat red blood cell), proper division does not occur. Also elliptical cells are sometimes cut in half (lower middle image).?Any ideas how I could correct this?
>
> Thanks
>
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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[gankaku]

Dear Clay,

as Niko mentioned the watershed Irregular Features might help. but its
purpose is to prevent overfragmentation as sometimes produced by the normal
watershed algorithm in ImageJ.
Nevertheless, it is based on the normal watershed. So if your connections
will not be split up correctly by the normal watershed you will also hit
the limit with the toolbox watershed.

There is another adjustable watershedding algorithm from Michael Schmid (if
I am not wrong) which is also worth a trial.

cheers,
Jan

2015-03-19 22:36 GMT+01:00 Clay Morton <
[hidden email]>:

>  Hey good people, I was wondering if anyone knew of a way to successfully
> separate touching particles that are not circular is shape. It seems that
> the water-shedding function only separates touching particles if they are
> circular, but has difficulty in correctly separating different shapes.
> Attached is an image that I have been working with. As you can see when a
> "crescent" shaped cell (sickle cell) is touching a circular cell (flat red
> blood cell), proper division does not occur. Also elliptical cells are
> sometimes cut in half (lower middle image).?Any ideas how I could correct
> this?
>
> Thanks
>
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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CEO: Dr. rer. nat. Jan Brocher
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[Ignacio Arganda-Carreras]

Hello Clay,

You can also give a try to the Morphological Segmentation plugin:
http://fiji.sc/Morphological_Segmentation

Best,

ignacio

On Fri, Mar 20, 2015 at 9:15 AM, Niko Ehrenfeuchter <
[hidden email]> wrote:

> Dear anonymous,
>
> you could have a look at Jan Brocher's "Irregular Watershed":
>
> http://fiji.sc/BioVoxxel_Toolbox#Watershed_Irregular_Structures
>
> Cheers
> Niko
>
>
> On 19.03.2015 22:36, Clay Morton wrote:
>
>>   Hey good people, I was wondering if anyone knew of a way to
>> successfully separate touching particles that are not circular is shape. It
>> seems that the water-shedding function only separates touching particles if
>> they are circular, but has difficulty in correctly separating different
>> shapes. Attached is an image that I have been working with. As you can see
>> when a "crescent" shaped cell (sickle cell) is touching a circular cell
>> (flat red blood cell), proper division does not occur. Also elliptical
>> cells are sometimes cut in half (lower middle image).?Any ideas how I could
>> correct this?
>>
>> Thanks
>>
>>
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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Ignacio Arganda-Carreras, Ph.D.
Seung's lab, 46-5065
Department of Brain and Cognitive Sciences
Massachusetts Institute of Technology
43 Vassar St.
Cambridge, MA 02139
USA

Phone: [phone]
Website: http://bioweb.cnb.csic.es/~iarganda/index_EN.html

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