Concave particle correction

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Concave particle correction

knels
Hello,

I am wondering if anyone would know how to get imagej to automatically
connect concave regions of particles for analysis without manually tracing a
connecting line. The first attached image has a couple of particles that
have concave regions I would like to bridge/fill before I measure. The
second image is an idea of what a finished particle would look like. Is
there a general function that does this?

<http://imagej.1557.x6.nabble.com/file/t381542/1.jpg>
<http://imagej.1557.x6.nabble.com/file/t381542/2.jpg>


Thanks!
Knels



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Re: Concave particle correction

Cammer, Michael
Edit > Selection > Convex hull

//setTool("wand");
doWand(196, 92);
run("Convex Hull");

Michael Cammer, Research Scientist, DART Microscopy Laboratory
NYU Langone Health, 540 First Avenue, SK2 Microscopy Suite, New York, NY  10016
C: 914-309-3270  [hidden email]    http://microscopynotes.com/ 
https://med.nyu.edu/research/research-resources/scientific-cores-shared-resources/microscopy-laboratory


-----Original Message-----
From: knels [mailto:[hidden email]]
Sent: Monday, October 30, 2017 5:08 PM
To: [hidden email]
Subject: Concave particle correction

Hello,

I am wondering if anyone would know how to get imagej to automatically connect concave regions of particles for analysis without manually tracing a connecting line. The first attached image has a couple of particles that have concave regions I would like to bridge/fill before I measure. The second image is an idea of what a finished particle would look like. Is there a general function that does this?

<https://urldefense.proofpoint.com/v2/url?u=http-3A__imagej.1557.x6.nabble.com_file_t381542_1.jpg&d=DQICAg&c=j5oPpO0eBH1iio48DtsedbOBGmuw5jHLjgvtN2r4ehE&r=oU_05LztNstAydlbm5L5GDu_vAdjXk3frDLx_CqKkuo&m=bSE0qf-5qhxa90CC2v5whb9663Ai3KkDynUHImAbl_g&s=MpLt2BfuH20yD0UAzxDlieRdQdIr5HRBytwxZElZYno&e= > <https://urldefense.proofpoint.com/v2/url?u=http-3A__imagej.1557.x6.nabble.com_file_t381542_2.jpg&d=DQICAg&c=j5oPpO0eBH1iio48DtsedbOBGmuw5jHLjgvtN2r4ehE&r=oU_05LztNstAydlbm5L5GDu_vAdjXk3frDLx_CqKkuo&m=bSE0qf-5qhxa90CC2v5whb9663Ai3KkDynUHImAbl_g&s=t5K5Y-6041K7FTmrzoQg6tsIAA26H3mpBQVqXcnFbGM&e= >


Thanks!
Knels



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Re: Concave particle correction

Herbie
In reply to this post by knels
Good day Knels,

perhaps not exactly what you have in mind but perhaps sufficiently close:

0. Make sure that the foreground drawing color is black
1. Make sure that your image is really binary
    (JPG-compressed images generally are *not*)
2. Select a single object by use of the Wand-tool
3. "Edit >> Selection >> Convex Hull"
4. "Edit >> Draw"

You may also try the binary operations available in ImageJ.

HTH

Herbie

:::::::::::::::::::::::::::::::::::
Am 30.10.17 um 22:08 schrieb knels:

> Hello,
>
> I am wondering if anyone would know how to get imagej to automatically
> connect concave regions of particles for analysis without manually tracing a
> connecting line. The first attached image has a couple of particles that
> have concave regions I would like to bridge/fill before I measure. The
> second image is an idea of what a finished particle would look like. Is
> there a general function that does this?
>
> <http://imagej.1557.x6.nabble.com/file/t381542/1.jpg>
> <http://imagej.1557.x6.nabble.com/file/t381542/2.jpg>
>
>
> Thanks!
> Knels
>
>
>
> --
> Sent from: http://imagej.1557.x6.nabble.com/
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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Re: Concave particle correction

knels
Awesome thank you so much that did the trick!

-Knels



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