Help in Applying ImageJ

[Bourg, Fred {FLNA}]

Hello all,

I am looking for some help characterizing regions within images.

I have a large number of images that I need to analyze.

The images are of randomly spaced particles that cover approximately 20-30% of the total image area (1024X1024).  I need to analyze each of the particles individually and then analyze the background in all three planes (R, G, and B).  Alternatively, I can convert to CIE L*, a*, b* but I prefer to work in the RGB space for now.  Ideally, I'd like to have statistics for each individual particle and the background.  Initially, by statistics, I can go with something as simple as mean and standard deviation for each channel, but other meaningful statistics regarding size, shape, overall particle density as a percent of total image, mean particle size, mean particle size standard deviation, and etc. would be helpful for the overall image.  Statistics on f individual particles related to size and color properties would be valuable information as well.  I'd also like to filter out spots and specs based on a size that I can set based on evaluating the raw image, but it should have a default value of 50 pixels.  Any particle smaller in size than this filter value should be removed from the background calculations as well.  Statistics on the number and size of particles filtered out of the analysis (number, mean size, standard deviation of size, and total number of pixels excluded by the filter would also be of value.

As I literally have thousands of images to analyze, I'd like to be able to specify a folder that contains a set of images to be analyzed.  The output can be stored as individual files in the same folder.  I would like to have a single file that contains the statistics for the background of each image in the order analyzed in a format that can be exported to Excel for further analysis. Each row would be labeled with the original file name and there would be columns for each statistic (mean, Standard deviation for each channel, etc.) (Sample below)

                                                Background                                                 Particles                                                                                Spots
                        ___________________________     _________________________________             _______________________________
Filename       Ravg   Rstd    Gavg  Gstd   Bavg   Bstd    Part-Count   Part-AvgSize            Part-Stdsize             Spots Count   Spotsavgsize   Spotsstdsize
Image01       162     25       175     20       120     15              315               534                             89                                       25                       10                     3
Image02       156     21       163     24       134     10              178               876                             234                                      8                         32                     8
Etc.

I appreciate your help and perspectives on the feasibility of this analysis using this tool as I'm just getting started and am impressed with what I've been able to do so far.

Thanks in advance for your input and help.

Wilfred M. Bourg Jr., P.E.
Sr. Research Fellow
Pepsico



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