imageJ_wholeBrainAtlas
Package for ImageJ to have analysis output of RoiManagerX which is equivalent to ImageJ's native ROI manager with added functionality for brain mapping. And downstream analysis of the data
TODO
* work on documentation of README
* work on aggregation documentation
Protocols
The protocol folder contains series of protocol initially used for quantfication and registration of cells using imageJ. The prefered method is now to use wholebrain
ImageJ RoiManager X
* Java and ImageJ need to be installed for the pluglin to work
* The extracted plugin can then be copied into the ImageJ/Fiji plugin folder
* Most of the development is located in the subfolder `edu/scripps` within the RoiManager X
Downstream aggregation
* `forPostProcessing.py`enables file aggregation of exported output