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README.md

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+# DIPLOMAT
+
+Deep learning-based Identity Preserving Labeled-Object Multi-Animal Tracking.
+
+**NOTE:** DIPLOMAT is currently early beta software, there may be minor bugs and usability issues.
+
+If you are a user (not a developer contributing code), you may want to visit:
+- the software website: [https://wheelerlab.org/DIPLOMAT](https://wheelerlab.org/DIPLOMAT/)
+- in-depth documentation: [https://diplomat.readthedocs.io](https://diplomat.readthedocs.io/en/latest)
+
+## About
+
+DIPLOMAT provides a multi-animal pose estimation and editing interface. It relies on a trained CNN model (currently supporting SLEAP and DeepLabCut packages) and uses algorithms to first _**Track**_ the animal body part in a way that reduces body part losses and identity swaps, and then provides an intuitive and memory/time efficient _**Interact**_ interface to edit and re-track as needed. DIPLOMAT differs from other multi-animal tracking packages by working directly off of confidence maps instead of running peak detection, allowing for more nuanced tracking results.
+
+![UI Demo Showing user correcting tracking in a video](interact_retrack_gif.gif)
+
+**Correcting and rerunning the Viterbi algorithm on the Interact Interface**
+
+| Example of tracking 2 Degus in a Box | Example of tracking 3 Rats |
+|:------------------------------------:|:--------------------------:|
+| ![Example of tracking 2 Degus](https://raw.githubusercontent.com/TravisWheelerLab/DIPLOMAT/main/docs/source/_static/imgs/example1.png) | ![Example of tracking 3 Rats](https://raw.githubusercontent.com/TravisWheelerLab/DIPLOMAT/main/docs/source/_static/imgs/example2.png) |
+## Installation
+
+DIPLOMAT also includes four environment configuration files for setting up DIPLOMAT with 
+[mamba](https://mamba.readthedocs.io/en/latest/installation/mamba-installation.html), which can
+be installed on Windows, Linux, or MacOS using the [Miniforge](https://github.com/conda-forge/miniforge) installer.
+To create an environment using mamba, run one of these four commands:
+```bash
+# Create the environment for using DIPLOMAT with DeepLabCut
+# GPU:
+mamba env create -f https://raw.githubusercontent.com/TravisWheelerLab/DIPLOMAT/main/conda-environments/DIPLOMAT-DEEPLABCUT.yaml
+# CPU only:
+mamba env create -f https://raw.githubusercontent.com/TravisWheelerLab/DIPLOMAT/main/conda-environments/DIPLOMAT-DEEPLABCUT-CPU.yaml
+# OR Create an environment for using DIPLOMAT with SLEAP instead...
+# GPU:
+mamba env create -f https://raw.githubusercontent.com/TravisWheelerLab/DIPLOMAT/main/conda-environments/DIPLOMAT-SLEAP.yaml
+# CPU only:
+mamba env create -f https://raw.githubusercontent.com/TravisWheelerLab/DIPLOMAT/main/conda-environments/DIPLOMAT-SLEAP-CPU.yaml
+```
+And then activate the environment with one of these two commands:
+```bash
+# Activate the DeepLabCut/DIPLOMAT environment...
+mamba activate DIPLOMAT-DEEPLABCUT
+# Activate the SLEAP/DIPLOMAT environment...
+mamba activate DIPLOMAT-SLEAP
+```
+
+For a more thorough explanation of the installation process and alternative installation methods, see the 
+[documentation](https://diplomat.readthedocs.io/en/latest/installation.html).
+
+## Usage
+
+#### Running DIPLOMAT
+
+To run DIPLOMAT on a video once it is installed, simply use DIPLOMAT's `unsupervised` and `supervised` commands to track a video:
+```bash
+# Run DIPLOMAT with no UI...
+diplomat track -c path/to/config -v path/to/video
+# Run DIPLOMAT with UI...
+diplomat track_and_interact -c path/to/config -v path/to/video
+```
+
+Multiple videos can be tracked by passing them as a list:
+```bash
+diplomat track -c path/to/config -v [path/to/video1, path/to/video2, "path/to/video3"]
+```
+
+Once tracking is done, DIPLOMAT can create labeled videos via it's `annotate` subcommand:
+```bash
+diplomat annotate -c path/to/config -v path/to/video
+```
+
+If you need to reopen the UI to make further major modifications, you can do so using the interact subcommand:
+```bash
+diplomat interact -s path/to/ui_state.dipui
+```
+This displays the full UI again for making further edits. Results are saved back to the same files.
+
+If you need to make minor modifications after tracking a video, you can do so using the tweak subcommand:
+```bash
+diplomat tweak -c path/to/config -v path/to/video
+```
+This will display a stripped down version of the interactive editing UI, allowing for minor tweaks to be made to the 
+tracks, and then saved back to the same file.
+
+For a list of additional ways DIPLOMAT can be used, see the [documentation](https://diplomat.readthedocs.io/en/latest/basic_usage.html).
+
+#### Additional Help
+
+All DIPLOMAT commands are documented via help strings. To get more information about a diplomat subcommand or command, simply run it with the `-h` or `--help` flag.
+
+```bash
+# Help for all of diplomat (lists sub commands of diplomat):
+diplomat --help 
+# Help for the track subcommand:
+diplomat track --help
+# Help for the predictors subcommand space:
+diplomat predictors --help
+```
+
+## Documentation
+
+DIPLOMAT has documentation on ReadTheDocs at [https://diplomat.readthedocs.io/en/latest](https://diplomat.readthedocs.io/en/latest).
+
+## Development
+
+DIPLOMAT is written entirely in python. To set up an environment for developing DIPLOMAT, you can simply pull down this repository and install its
+requirements using pip. For a further description of how to set up DIPLOMAT for development, see the 
+[Development Usage](https://diplomat.readthedocs.io/en/latest/advanced_usage.html#development-usage) section in the documentation.
+
+## Contributing
+
+We welcome external contributions, although it is a good idea to contact the
+maintainers before embarking on any significant development work to make sure
+the proposed changes are a good fit.
+
+Contributors agree to license their code under the license in use by this
+project (see `LICENSE`).
+
+To contribute:
+
+  1. Fork the repo
+  2. Make changes on a branch
+  3. Create a pull request
+
+## License
+
+See `LICENSE` for details.
+
+## Authors
+
+If you have any questions, feel free to reach out to George Glidden, at [[email protected]](mailto:[email protected])
+
+See `AUTHORS` the full list of authors.
+