This repository contains the code needed to process images of suspended particles for sizing. The base code can be used on any set of images, but the focus of the material contained in the repository is to provide a workflow for processing FlocARAZI profile data. The FlocARAZI is an imaging system that was designed for the measurement of flocculated suspensions of mud in natural environments. Detailed information on the development and use of the FlocARAZI can be found in the following paper:
Osborn, R., Dillon, B., Tran, D., Abolfazli, E., Dunne, K. B. J., Nittrouer, J. A., & Strom, K. (2021). FlocARAZI: An in-situ, image-based profiling instrument for sizing solid and flocculated suspended sediment. Journal of Geophysical Research: Earth Surface, 126, e2021JF006210. doi: 10.1029/2021JF006210 [Data and build instructions]
Detailed instructions on how to use code provided in this repository for processing FlocARAZI data can be found in the following Google Doc Manual for the repository.
Requirements to run
- Python
- ImageJ and Java
The default data to be processed is a subsample of SampleData/2022-04-17-Seine-Day1-Cast4. This contains 657 images collected over a depth in the Seine Estuary.
To test the image processing alone (no integration of CTD data for the development of a profile), try processing the images in SampleData/Mud-SieneCast04-small.
For processing and visualization of data not associated with vertical profiles over the water columns or time series at a point, use only the code in the folder \0_Standard_Processing. Details regarding the use of the code in the folder \0_Standard_Processing can also be found in the following Google Doc Manual.