Hi Miguel,

If you would be willing to post an example image, I'd be happy to make a segmentation recipe file using new software MIPAR, available at MIPAR.us, to do exactly what you need. There are actually several other researchers at Iowa State using MIPAR for their own image analysis work.

Cheers,

John

Hello John, of course. I generate images similar to this one, this was published by

Emanuel Carrilho, but my images are really similar. So, I want to measure basically the color intensity within the square. Preferably by using channel green or blue. I will check for the software you mentioned. Thank you !

You can also record a macro with ImageJ and process all your images in batch

Design a software yourself rather than than getting one done by somebody else.

Hi Miguel,

Thanks very much for posting. So to clarify, you want the color intensity measured within each small square? And how do you define "color intensity"? Of the green channel, blue channel, or both?

Cheers,

John

Hey John, yes within the square. I would like to have green channel first but I would like to be able to choose the channel as well. 

Hi Miguel,

Here is what I came up with in MIPAR:

1) A MIPAR recipe to automatically find each colored box

2) A screenshot of the end result of the recipe

3) The average green channel intensity of each box overlaid on a color scale on the green channel of the original image

4) The spreadsheet of green channel box intensities

5) A cropped version of the original image that I used

Please let me know of any other questions!

Cheers,

John