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A benchmarked comparison of software packages for time-lapse image processing of monolayer bacterial population dynamics

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ImageProcessing-Benchmarking

In this repository, you will find the following folders:

Individual Package Folders: Each package has a dedicated folder where outputs for each dataset are stored. Inside these, there's a subfolder named "Analyses", which includes tracking plots for each package and post-processing analyses.

Ground Truth: Contains data related to reference masks for segmentation ground truth, along with data for tracking ground truth.

Ilastik-training-files: Stores data associated with the output from Ilastik, used as input for FAST and CP.

Raw-Images: Houses all datasets of raw images and inputs.

Pipelines: This folder includes the pipeline for each package utilized in this study.

Scripts: Contains individual README files offering guidance for each script. These scripts are for the analyses in the study titled "A benchmarked comparison of software packages for time-lapse image processing of monolayer bacterial population dynamics".

For additional information, please feel free to reach out to atiyeh.ahmadi@uwaterloo.ca

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A benchmarked comparison of software packages for time-lapse image processing of monolayer bacterial population dynamics

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