I was hoping you would be able to offer some guidance on what the best method might be to achieve what I need. This is my fist foray into the world ImageJ and I look forward to building my understanding!
So I have 6 images from a Scanning Electron Microscope at x100 magnification http://imgur.com/a/x7bhG. As you can see on the images, the black deposits or plaques are colonies of attached bacteria.
What I would like to do is try to find out the surface area (absolute as well as fraction) occupied by the bacterial colonies. I did a bit of googling and discovered that thresholding would be the best way to achieve this.
Firstly, is that right?
The method I used was to first load up the picture. Then change image type to RGB stack. After this I went to adjust and thresholding and manually changed the min and max parameters so that “visually” all of the bacteria were covered (red).
Secondly, I need to compare the area occupied by bacteria on the different surfaces. However because the pictures all are coloured slightly differently this means setting different thresholds values for each picture, and as I have just been doing this by eye, it is not ideal. So is there a way I can standardise the approach, to keep it consistent between the pictures? Maybe editing the pictures so they are all the same contrast before thresholding, or apply certain filters?
Any help would be greatly appreciated!!