I would like to count cells and, if possible, measure cell area near the epithelium using ImageJ. These should be used to calculate cell-density/mm2 in histological sections. My method is:
- 8-bit image
- Automatic adjustment of contrast and background.
- In plugin menu choose Particles Analysis- -- nucleus counter.
- Particle size 50 to 500 pixel 20x image 1950 x 1400 pixels.
- Add particles to multimeasure ROI.
- Get results.
This works alright but counts the cells in the adjacent epithelium. I need only connective tissue cells. Is there a way to use a selection tool, preferably a wide line selection tool, with my approach?
Simple way as already proposed by Mikheil:
1. draw ROIs for all areas to be analysed and add to ROI-Manager
2. measure the ROI areas
3. write / record macro:
- duplicate whole image
- choose ROI from ROI-Manager
- use Clear outside
- do thresholding
4. do your measurement
5. you can repeat this for as much ROIs you have (simply by using shortcut keys)
Otherwise you will need to write a little macro going through all the ROIs defined by you in step 1 and save the results in separate tables.
However, I never used the Nucleus Counter, so you will have to look into this.
This should work.
Cheers
Jochen
Yes, but you can simply "erase" unnecessary image areas from figure (For eg. in Photoshop or other image editing soft).
@Mikheil. You are right for just the measurment. But i need the density as will, i. e. number of cells and area fraction per mm2. The images are taken at epithelial mesenchymal interface. There fore area selection is needed.
Maybe using the Colour Deconvolution BEFORE the particle counter would help to separate originally!
Look it up here: http://imagejdocu.tudor.lu/doku.php?id=plugin:color:colour_deconvolution:start
Unless there's an appreciable difference in the size of the two cell-types, I'm afraid it won't be useful.
You could go on a counting-spree using the Cell Counter under Plugins>Analyse.
I would also recommend using Cell Profiler if that can help. You can create modules to first count all cells and then to count a subset of those cells differing in cell size or intensity or some such parameter.
Good luck with this!
Simple way as already proposed by Mikheil:
1. draw ROIs for all areas to be analysed and add to ROI-Manager
2. measure the ROI areas
3. write / record macro:
- duplicate whole image
- choose ROI from ROI-Manager
- use Clear outside
- do thresholding
4. do your measurement
5. you can repeat this for as much ROIs you have (simply by using shortcut keys)
Otherwise you will need to write a little macro going through all the ROIs defined by you in step 1 and save the results in separate tables.
However, I never used the Nucleus Counter, so you will have to look into this.
This should work.
Cheers
Jochen
How to do stereological approach with cross section histological specimen Mr. Lambros Panagis? Can you explain? I haven't basic knowledge in image analysis with stereological analysis
@El-Hassan Shabana. Jochen Neuhaus proposed good algorithm and you can try to create macro or toolset for automatic or semiautomatic measuring
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