BATS is a Bioimage Annotation Tool for Segmentation in microscopy imaging.
BATS is the continuation of the Data-Centric Platform (DCP). The repository was renamed and restructured. The current BATS repository represents the actively maintained version of the project. For older version and commit history please checkout the older repo.
This repo includes a client and server side for using our Bioimage Annotation Tool for Segmentation (BATS). The client and server communicate via the bentoml library. The client interacts with the server every time we run model inference. For full functionality of the software the server should be running, either locally or remotely.
To install and start the server side, follow the instructions described in BATS Server Installation & Launch.
To run the client GUI follow the instructions described in BATS Client Installation & Launch.
For an overview of both components and their interaction with the step-by-step guide and screen shots, visit our documentation page.
BATS handles all kinds of segmentation tasks! Try it out if you need to do:
- Instance segmentation
- Semantic segmentation
- Multi-class instance segmentation
This repo includes the data/ directory with some toy data which you can use as the Uncurated dataset folder. You can create (empty) folders for the other two directories required in the welcome window and start playing around.
Our platform encourages the use of data centric practices. With the user friendly client interface you can:
- Detect and remove outliers from your training data: only confirmed samples are used to train our models
- Detect and correct labeling errors: editing labels with the integrated napari visualisation tool
- AI-assisted labelling: Apply any changes to your labels faster using SAM prompts
- Auto cleanup: Left over pixels remaining after using the eraser tool or an object your forgot to add a class label to? BATS will let you know and clean everything up for you!
- Establish consensus: allows for multiple annotators before curated label is passed to train model
- Focus on data curation: no interaction with model parameters during training and inference
If you use BATS (Bioimage Annotation Tool for Segmentation) in your work, please cite it as:
Christina Bukas, Helena Pelin, Haider Khan, Marie Piraud. (2026). Bioimage Annotation Tool for Segmentation (BATS) (Version v.0.1.0). Zenodo. https://doi.org/10.5281/zenodo.19203946
@software{bats_2026,
author = {{Christina Bukas, Helena Pelin, Haider Khan, Marie Piraud}},
title = {Bioimage Annotation Tool for Segmentation (BATS)},
year = {2026},
version = {v.0.1.0},
publisher = {Zenodo},
doi = {10.5281/zenodo.19203685},
url = {https://doi.org/10.5281/zenodo.19203685}
}