A set of macros for ImageJ and objectJ to analyze quadrats in ecology.
For the moment it is only for temperate corals and algae (what I am working on) and use the random points methods. It is heavily inspired by CPCe (http://www.nova.edu/ocean/cpce/) but because this one is not free (libre) software and runs only under windows, I decided to start using imageJ (http://imagej.nih.gov/). The cell counter in imageJ was not enough and I used and modify the cell counter of the plugin objectJ (http://simon.bio.uva.nl/objectj/) to fit my needs.
To use it download the project file and open it with imageJ, I tested it with imageJ 1.48t and objectJ 1.03m
From objectj:
- Allow non destructive marking of quadrat photos
- Produce the count results for each object
Customization:
- The project include categories suitable for temperate corals ecosystems in Shimoda, these categories are easily changeable but need to edit the macro file to change the shortcut.
- Draw a user defined number of random points on all the photos (see ToDo)
- Draw 64 points (8*8) on a grid within the user defined quadrat zone.
- Make the number of points for the grid variable
- Add an if check if slope of the qudarat frame are 0 or infinity to be able to draw the grid in these case.
- User-Defined zone for random points
- Write the documentation
- Add the possibility to remove all markers elsewhere than in the objectj menu
- Add the possibilty to edit the object which will automatically edit the shorcut.
- Add the tracing area methods. but it is already possible in imageJ alone
- One day perhaps...completely fork objectj and create an independant plugin, if it seems good.