COMMERCIAL POST RE: Phase contrast image segmentation

[Trevor Lancon]

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Hi Zdenek,

An alternative to Robert's approach is to use a pixel classifier. Here is a screenshot of some quick (~30 second) training regions vs the final segmentation in Aivia:

https://drvtechnologies-my.sharepoint.com/:i:/p/trevorl/ERNWr7j_XKlAv05k36DUDvUB_8GFsrYyLSbDA4k1oz4q0g?e=2wo6Y0

Free tools (that I know of) that offer this are Aivia Community, ilastik, QuPath, and the WEKA plugin for ImageJ. For color images like this one, it's probably best to include all channels (R, G, and B) in the training set in case the white balance is off. Trained classifiers can usually be batch applied across many images.

Best regards,

Trevor

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Trevor Lancon
Aivia Applications Specialist - Eastern US
[hidden email] | [phone]

-----Original Message-----
From: Confocal Microscopy List <[hidden email]> On Behalf Of [hidden email]
Sent: Tuesday, September 15, 2020 4:46 PM
To: [hidden email]
Subject: Re: Phase contrast image segmentation

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Dear Zdenek,

I recently gave an online lecture introducing students to basic ImageJ Macro where we process very similar images:

https://youtu.be/q4ISEWq6q4E

Also check out image.sc for alternate approaches:

https://forum.image.sc/t/cell-segmentation-in-phase-contrast/943/14<https://forum.image.sc/t/cell-segmentation-in-phase-contrast/943/14?u=haesleinhuepf>

I'm sure there are more sophisticated plugins and tools for processing that kind of data, especially on python side, but maybe that's a starting point.

Cheers,
Robert


--
Robert Haase, Dr. rer. medic.
Post-doc, Myers Lab

Center for Systems Biology Dresden
Max Planck Institute of Molecular Cell Biology and Genetics Pfotenhauerstr. 108
01307 Dresden


________________________________
From: Zdenek Svindrych <[hidden email]> on behalf of Zdenek Svindrych <[hidden email]>
Sent: Tuesday, 15 September 2020, 23:35
To: [hidden email]
Subject: Phase contrast image segmentation

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Dear Listers,

not exactly a confocal question, but here it goes: Do you know of a simple, reliable, or even barely useable way to segment transmitted light images of yeast or bacteria, such as this one?:
https://drive.google.com/file/d/15ke38DZsADu8ahL9m1WzBEiIxIsBzj8O
Preferably in ImageJ, but I'm happy to try other platforms.

Thanks!

Best, zdenek
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Zdenek Svindrych, Ph.D.
Research Scientist - Microscopy Imaging Specialist Department of Biochemistry and Cell Biology Geisel School of Medicine at Dartmouth