Hi All,
I want to use imageJ and program it identify an object as a cell from an image and count all the other object that have the same parameters/measures as the object i initially specified??
In the image i attached, Say i want imageJ to identify this object ( in yellow circle) and measure all object that have similar size or shape in the rest of the image ??
This would be easier done in CellProfiler. You can set a range of parameters in the IdentifyPrimaryObject module and have it count all objects that fall within those parameters.
www.cellprofiler.org
Thanks Jordan but how to do this in cell Profiler ??? It doesn't seem to accept JPG images.
As JPG images are lossy files, they do not accurately hold scientific raw data. It is better to use TIFF or even PNG files. I have not tried to load JPG files into CellProfiler, but I would expect it should at least load it, just not preferably.
You can convert files using ImageJ quite easily, but again, if your data is stored in a JPG to begin with, you are already in a lossless regime wherein your data may not represent ground-truth.
You can measure cells (by number, fluorescence, shape etc) with ImageJ. Therefore, images must be converted into 8-bit images (Image, Type, 8 bit) and adjusted to a lower and upper (Pixel) threshold (Image, Adjust, Threshold, Set or Auto). Using the analyze particle tool (Analyze, Analyze Particles), the number of fluorescent spots/cells can be counted automatically.
Sherief you will need better pictures for image analysis, no matter what software you use. The picture you attached is clearly out of focus and the cells are not in a monolayer. You cannot count them properly by software if they overlap like that.
So double check your focus before taking picture and choose a good area with cells nicely spaced or at least not overlapping. Or plate fewer cells to begin with, depending on your protocol.
Dear Sherief,
I think that link http://imagejdocu.tudor.lu/doku.php?id=video:analysis:particle_counting_-_automated_and_manual
will help you to solve the problem, or to get an idea how to solve the problem.
Best Soenke
I would look into R packages for segmentation and feature extraction. Specifically packages imageHTS and phenoDessim.
hello,
Johanna Meyer
I use ImageJ as you described but I want to ask a question if I want to analyze for example just macrophages how I can know the size of cells that I interested in to set a lower and upper (Pixel) ???????
thanks so much