Posted by
ctrueden on
URL: http://imagej.273.s1.nabble.com/counting-cells-tp5001091p5001100.html
Hi Thuraya,
> i need help how to count cells with the dark purple color that exist
> in the big circle area
Did you try Fiji's Color Threshold plugin? I tried it with your sample
image and got pretty good results with the following settings:
Hue: 186 - 216
Saturation: 0 - 255
Brightness: 0 - 180
You can then create a selection & mask and manipulate them in a variety of
ways:
- Click the Select button in the Threshold Color dialog to create a
selection.
- Run the following plugins (press L for command finder):
-- Create Mask
-- Fill Holes (on the binary image)
-- Watershed (chops up blobs into convex shapes/cells)
-- Analyze Particles... (on the binary image, same options as above)
--- Size: 10-Infinity
--- Display results
--- Clear results
--- Add to Manager
--- Exclude on edges
Now you have your cells in the ROI Manager, so you can:
- Close Mask window (Don't save)
- Close Results window
- Finally, in ROI Manager window, check Show All and Labels boxes
Your original image will show the cell outlines. To measure them, run:
- Run "Set Measurements..." (to configure which statistics are calculated)
- Click "Measure" button in ROI Manager
Now your measurements will be based on the original data, using the ROIs
(cells) from the ROI Manager.
Here is a screenshot of the cells I segmented using the above procedure:
http://code.imagej.net/curtis/fiji-particles.jpgThat was just a quick attempt (e.g. a few of the cells are fused, and there
are some overly-small cells). You can do better by tweaking further with
the Threshold Color settings, and using a bigger minimum Size (perhaps
"25-Infinity"?) in the Analyze Particles dialog.
You could also try CellProfiler (
http://cellprofiler.org/); it has many
good techniques for this sort of thing.
Regards,
Curtis
On Mon, Dec 10, 2012 at 5:53 AM, Thuraya Medhat <
[hidden email]>wrote:
--
ImageJ mailing list:
http://imagej.nih.gov/ij/list.html