Recording file name in "Cell counter" plug in

[Jameel Ahmad Khan]

Hello everyone,
I am using "cell counter" plug in of ImageJ  for counting different cell types in my image data.
Basically what I am doing is: counting different cell types in a particular field (images). In order to achieve statistically significant counts, I have to do this for a large number of fields (often more than 30) for each sample.
   Though the Cell counter plugin is proving to be really useful but life would be a lot easier if it is possible to have a module in this plugin which also records source file name along with Counter type. This will not only enable:
1. The cross checking/correction of the results after finishing the counting (immediately as well as at later time point).
2. Make the plug in more useful for counting cells from multiple files.

I will really appreciate if some one can suggest/provide a macros/patch/update in cell counter plugin for this purpose.

PS: I am just a beginner in image data with practically no experience in programming so a stepwise instructions of use will be greatly appreciated.

With best regards
Jameel

[Nathaniel Ryckman]

Jameel Ahmad Khan wrote

Hello everyone,
I am using "cell counter" plug in of ImageJ  for counting different cell types in my image data.
Basically what I am doing is: counting different cell types in a particular field (images). In order to achieve statistically significant counts, I have to do this for a large number of fields (often more than 30) for each sample.
   Though the Cell counter plugin is proving to be really useful but life would be a lot easier if it is possible to have a module in this plugin which also records source file name along with Counter type. This will not only enable:
1. The cross checking/correction of the results after finishing the counting (immediately as well as at later time point).
2. Make the plug in more useful for counting cells from multiple files.

I will really appreciate if some one can suggest/provide a macros/patch/update in cell counter plugin for this purpose.

PS: I am just a beginner in image data with practically no experience in programming so a stepwise instructions of use will be greatly appreciated.

With best regards
Jameel

My recommendation for you is to give the CellProfiler a try if you can't find a plugin that you would like to use. The CellProfiler software is good for people who do not have programming experience and who are dealing with inaccuracies by using large populations/controls.

The imageJ software is good for people who are doing measurements by hand or have programming experience. It's more flexible but, consequently, also more complicated.

If you had just wanted to output the source file name, I would have recommend that you follow some of the macro tutorials and then create a simple macro:

http://rsbweb.nih.gov/ij/developer/macro/macros.html
http://rsbweb.nih.gov/ij/developer/macro/functions.html

The problem, however, is that you want the cell types. ITCN does not do a thorough analysis of the cells from my understanding. What it does is it chooses the brightest spots on your picture to count your cells (aka maxima).

If you wanted to analyze characteristics of your cells, you could use the following menu commands:

Threshold or AutoThreshold ->  Binarize -> Watershed -> Particle Analyzer -> Multi Measurement -> Export to Excel

Unfortunately, this technique does not work well if your cells are very amorphous. I'm developing a more accurate method, but it still needs a little work:

http://imagej.588099.n2.nabble.com/file/n6400830/original.jpg
http://imagej.588099.n2.nabble.com/file/n6400830/p42-w2-f02.jpg

SUMMARY:
1) Check this page to see if it has a plugin that you would suite your needs http://rsbweb.nih.gov/ij/plugins/
2) Learn to program or use this software instead http://www.cellprofiler.org/

[Citron, Bruce]

One way it could be done, if you are using a macro to open each of the
different images in a series, would be to use the print command to enter the
opened file specification in a log window which can be saved or exported.
For example, if you have 10 images, image1, image2, ... , image10 where n =
the image number, filename = ³image² and filepath = ³the directory path to
that file²
open(filepath+filename+n);  will open the file and
Print(filepath+filename+n);  will write that information to a log window.

Bruce A. Citron, Ph.D., Bay Pines VA



On 5/26/11 7:32 , "Jameel Ahmad Khan" <[hidden email]> wrote:

> Hello everyone,
> I am using "cell counter" plug in of ImageJ  for counting different cell types
> in my image data.
> Basically what I am doing is: counting different cell types in a particular
> field (images). In order to achieve statistically significant counts, I have
> to do this for a large number of fields (often more than 30) for each sample.
>    Though the Cell counter plugin is proving to be really useful but life
> would be a lot easier if it is possible to have a module in this plugin which
> also records source file name along with Counter type. This will not only
> enable:
> 1. The cross checking/correction of the results after finishing the counting
> (immediately as well as at later time point).
> 2. Make the plug in more useful for counting cells from multiple files.
>
> I will really appreciate if some one can suggest/provide a macros/patch/update
> in cell counter plugin for this purpose.
>
> PS: I am just a beginner in image data with practically no experience in
> programming so a stepwise instructions of use will be greatly appreciated.
>
> With best regards
> Jameel