cell surface detection (segmentation) in bright field image and make it selected as ROI.

[Junsung LEE]

At present, I am trying to quantify fluorescent signal per a cell, but I have troubles in some parts. I would like to know the followings is possible :


1) segment cells (detect cell outline of surface) in bright field cell image "automatically".

2) make it selected as ROI.

3) transfer (or copy and paste) ROIs from bright field image to fluorescent image.

4) measure fluorescent signal intensity in ROI.


* Labeling cell surface with fluorescent dye is not an option because I already use all of color channel that I can apply.


Tracing out cell surface with polygon selections tool or freehand selections tool in fluorescent image directly is possible with limits, but it's gonna be not accurate when cell surface staining dye is not used.

I will be appreciated if you tell me how.


Thanks in advance, and I wish you the best in your experiments.

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[Jacqueline Ross]

Hi Junsung,

You may need to post an image somewhere in order to get a response. Segmentation in brightfield can be challenging so you probably need to do some edge detection to try to define the boundaries, e.g. Process - Find Edges and/or other filters. You may have to do some pre-processing prior to using the edge filter.

Once you have done that, the rest of your question should be fairly straightforward to answer using the ROI Manager options.

Kind regards,

Jacqui

Jacqueline Ross
Biomedical Imaging Microscopist
Biomedical Imaging Research Unit 
School of Medical Sciences 
Faculty of Medical & Health Sciences
The University of Auckland
Private Bag 92019
Auckland 1142, NEW ZEALAND

Tel: [phone]
Fax: [phone]

http://www.fmhs.auckland.ac.nz/sms/biru/

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Junsung LEE
Sent: Tuesday, 19 March 2013 2:52 p.m.
To: [hidden email]
Subject: cell surface detection (segmentation) in bright field image and make it selected as ROI.

At present, I am trying to quantify fluorescent signal per a cell, but I have troubles in some parts. I would like to know the followings is possible :


1) segment cells (detect cell outline of surface) in bright field cell image "automatically".

2) make it selected as ROI.

3) transfer (or copy and paste) ROIs from bright field image to fluorescent image.

4) measure fluorescent signal intensity in ROI.


* Labeling cell surface with fluorescent dye is not an option because I already use all of color channel that I can apply.


Tracing out cell surface with polygon selections tool or freehand selections tool in fluorescent image directly is possible with limits, but it's gonna be not accurate when cell surface staining dye is not used.

I will be appreciated if you tell me how.


Thanks in advance, and I wish you the best in your experiments.

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html