I have been using Image J for a number of years to analyse photographs of plants. The process by which I obtain the aerial visible area is as follows:
I photograph my plant and upload it into Image J and set the scale (Analyze > Set Scale):
I then adjust the colour threshold (Image > Adjust > Color Threshold …), shown below:
I then analyse particles (Analyse > Analyse Particles…). Usually all of the areas highlighted in red in the threshold image (above) will show in the Particle analysis (unless I use more stringent conditions), though now only part of the image is appearing. The part of the image that particles can be analysed from is not always the same. So in different images it is not always the bottom right hand corner that can be analysed, as shown in this example. This is the problem.
The process worked on Tuesday, however this begun to happen yesterday. I have since restarted my computer, and uninstalled to reinstall the software, but still the problem persists. Is there anyone out there who can help to get my analysis working correctly again?