MZB-WORFLOW: Macrozoobenthos data workflow suite
Welcome to the mzb-suite documentation! Here we introduce the package functionality and illustrate some examples of the Macrozoobenthos data processing workflow and suite mzb-suite.
Quickstart
To try out mzb-suite, the quickest way to is to spin a virtual session on RenkuLab, follow instructions for Online session on RenkuLab (only recommended for demo purposes).
If you want to install locally (recommended for day to day use), follow the instruction using Docker container (recommended for novice users) or Install libraries locally (advanced users).
To see how you can run the project scrips head over to How to use.
The MZB project
- Installation
How to install
mzb-suiteonline or on your machine.- How to use
How to work with the project, details about the workflows and its modules.
- Project structure
What does what in the project repository, and details about models used.
- Configuration
Explanation fo the configuration file and recommended parameter values.
- Best practices
Some tips on how to organise your project to make your life easier.
Gallery
- Demo of pipeline
Demonstration of
mzb-suitefeatures.
- Image segmentation
Example of extracting clips from large images
- Classification: inference
Example of automatically identifying taxa from organisms clips
- Skeletonization unsupervised
Example of extracting body length from organism clips
- Skeletonization: supervised, inference
Example of extracting body length and head width from organism clips
Scripts
- Processing scripts
Detailed explanation for processing functions
- Other scripts
Details of other convenience scripts
API reference
- mzbsuite module
Documentation on functions and parameters