Posted by
Majurski, Michael Paul (Fed) on
Aug 17, 2016; 2:33pm
URL: http://imagej.273.s1.nabble.com/Segment-phase-contrast-image-tp5017034p5017036.html
Laurent,
In the past I have broken the problem into two parts, first create a Foreground-Background mask (simpler task), and then leverage the mask to split apart single cells.
To obtain a Foreground-Background mask for phase-contrast I would suggest thresholding the image gradient.
In Fiji the command is called "Find Edges" (I have no idea where it is in the menu structure, I just use the Command Finder (
http://imagej.net/Using_the_Command_Launcher ) ).
Once you have the gradient you can apply the many thresholding methods Fiji has(
http://imagej.net/Auto_Threshold ) and see which one comes closest to your intuition of a correct segmentation.
This paper highlights our tool for doing just that (but with a new threshold selection method).
http://onlinelibrary.wiley.com/doi/10.1111/jmi.12269/full
There is a Fiji plugin implementation of this method available at our
https://isg.nist.gov activities page (EGT Segmentation).
Once you have your Foreground-Background mask, you can use it to guide a watershed based on pixel intensity (phase contrast cells tend to have a dark core and a bright halo).
This paper discusses our tool for performing single cell segmentation based on that approach and we have had success with phase contrast before.
https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-014-0431-xThis method is implemented in Matlab (with an executable that can be run without a Matlab license).
There is no guarantee that these tools will work with your images, but it is at least a place to start looking.
Good luck segmenting.
~Michael Majurski
-----Original Message-----
From: ImageJ Interest Group [mailto:
[hidden email]] On Behalf Of Laurent.guerard
Sent: Wednesday, August 17, 2016 09:56
To:
[hidden email]
Subject: Segment phase contrast image
Hi all,
I've been trying to segment a phase contrast image with no real success these past weeks.
The images are time series in order to track the movement of these cells.
Would any of you have ideas on how to it ?
Here is an example :
<
http://imagej.1557.x6.nabble.com/file/n5017034/TiledImage_T00_Trans.png>
There are 2 main problems with the images though :
1. There are dead cells/debris in the images which are very bright and might cause problems in the segmentation 2. The cells are really confluent, making it also difficult to separate close cells.
Any help would be welcome :)
Thanks.
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