I would also recommend ImageJ if you do not have the money for a commercial package. I routinely use the Fiji distribution of ImageJ (www.fiji.sc) and also regularly run workshops on using it. You can download the notes and demo images relevant to cell counting and segmentation from the following links. Cheers. Cam
https://dl.dropboxusercontent.com/u/11163658/Technical%20Note%2008%20-%20Cell%20Counting.pdf
https://dl.dropboxusercontent.com/u/11163658/Technical%20Note%2009%20-%20Cell%20Segmentation.pdf
https://dl.dropboxusercontent.com/u/11163658/Segmentation.zip
Http://www.cellprofiler.org/ http://www.cellprofiler.org/examples.shtml
As posted above, ImageJ or CellProfiler are preferred options. Whether you get useful results, however, depends on your raw data and the way you use the softwares. For cell counting, try to segment features that can be spatially separated easily. Typically, that would mean using object counting options applied to images of nuclear stains. If you go ahead with your analysis you will probably notice yourself that the seemingly simple task you have could turn out as a non-trivial problem. In fact, image segmentation and object identification is a big research focus in the area of 'computer vision'.
Hi... You can use Grid cell counter. It is free software. http://www.dnabaser.com/download/Cell-counter/grid-cell-counter.html
As posted by Georg Eschenburg you can use ImageJ with the addition of proper plugins. You will find attached instructions and plugin.
One final tool for image registration - give ilastik a go (http://www.ilastik.org/).. very easy to use and to train, and you can export the images to be counted in another package (eg imageJ or CellProfiler) very easily. Also, if you've never used ImageJ before, perhaps you might want to start with Fiji (http://fiji.sc/Fiji) which is just ImageJ but is tailored to image analysis. Good luck :)
I will also suggest imageJ...which is also free and very reliable software...
I would also recommend ImageJ if you do not have the money for a commercial package. I routinely use the Fiji distribution of ImageJ (www.fiji.sc) and also regularly run workshops on using it. You can download the notes and demo images relevant to cell counting and segmentation from the following links. Cheers. Cam
https://dl.dropboxusercontent.com/u/11163658/Technical%20Note%2008%20-%20Cell%20Counting.pdf
https://dl.dropboxusercontent.com/u/11163658/Technical%20Note%2009%20-%20Cell%20Segmentation.pdf
https://dl.dropboxusercontent.com/u/11163658/Segmentation.zip
I am sorry if this is no longer relevant, but I would strongly recommend you take a look at MIPAR at http://MIPAR.us. It is new, and very user friendly software we have just released as an extended free trial that has proven extremely capable at solving nearly any segmentation problem/image analysis problem we have faced. I am available any time to make a recipe file for you to jump start your analysis. Several tutorials are also available on the site. Very powerful for large batch processing as well. Hope we can help!
Fiji is the Best One Image Processing software -- its a distribution of Imagej http://fiji.sc/
I use Image Pro Plus V7.0. Its an old version of the software but the newer versions are more reliable and more easy to use. Overall, it's necessary to find out which method of staining would be better to use for staining the intended cells. I think, making the cells distinguishable is more important than the software that you are going to use.
How does imageJ work? I have downloaded it and when i double click on the icon nothing happens
Hello
Yes all these softwares ( Fiji , ImageJ and Image Pro Plus ) are good
I used Image Pro Plus software with IHC technic , Its depends on Integrated Optical Density (IOD) = area x average density
for image j there are two ways to count cells :
- Manual Cell Counting and Marking .
- Automated Counting of Single Color Images .
The details for these ways in the PDF
Good Luck
Saleh
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