Update base version

LICENSE

@@ -1,22 +1,28 @@
+BSD 3-Clause License
 
-The MIT License (MIT)
+Copyright (c) 2023, Howard Hughes Medical Institute
 
-Copyright (c) 2023 William Patton
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
 
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
 
-The above copyright notice and this permission notice shall be included in
-all copies or substantial portions of the Software.
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
 
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
-THE SOFTWARE.
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

README.md

@@ -1,67 +1,79 @@
-# napari-cellulus
+<h2 align="center">A napari plugin for cellulus</h2>
 
-[![License MIT](https://img.shields.io/pypi/l/napari-cellulus.svg?color=green)](https://github.com/funkelab/napari-cellulus/raw/main/LICENSE)
-[![PyPI](https://img.shields.io/pypi/v/napari-cellulus.svg?color=green)](https://pypi.org/project/napari-cellulus)
-[![Python Version](https://img.shields.io/pypi/pyversions/napari-cellulus.svg?color=green)](https://python.org)
-[![tests](https://github.com/funkelab/napari-cellulus/workflows/tests/badge.svg)](https://github.com/funkelab/napari-cellulus/actions)
-[![codecov](https://codecov.io/gh/funkelab/napari-cellulus/branch/main/graph/badge.svg)](https://codecov.io/gh/funkelab/napari-cellulus)
-[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-cellulus)](https://napari-hub.org/plugins/napari-cellulus)
+- **[Introduction](#introduction)**
+- **[Installation](#installation)**
+- **[Getting Started](#getting-started)**
+- **[Citation](#citation)**
+- **[Issues](#issues)**
 
-A Napari plugin for Cellulus: Unsupervised Learning of Object-Centric Embeddings for Cell Instance Segmentation in Microscopy Images
+### Introduction
 
-----------------------------------
+This repository hosts the code for the napari plugin built around **cellulus**, which was described in the **[preprint](https://arxiv.org/pdf/2310.08501.pdf)** titled **Unsupervised Learning of *Object-Centric Embeddings* for Cell Instance Segmentation in Microscopy Images**.
 
-This [napari] plugin was generated with [Cookiecutter] using [@napari]'s [cookiecutter-napari-plugin] template.
+*cellulus* is a deep learning based method which can be used to obtain instance-segmentation of objects in microscopy images in an unsupervised fashion i.e. requiring no ground truth labels during training.
 
-<!--
-Don't miss the full getting started guide to set up your new package:
-https://github.com/napari/cookiecutter-napari-plugin#getting-started
+The main source repository for *cellulus* lives **[here](https://github.com/funkelab/cellulus)**.
 
-and review the napari docs for plugin developers:
-https://napari.org/stable/plugins/index.html
--->
+### Installation
 
-## Installation
+One could execute these lines of code below to create a new environment and install dependencies.
 
-You can install `napari-cellulus` via [pip]:
+1. Create a new environment called `napari-cellulus`:
 
-    pip install napari-cellulus
+```bash
+conda create -y -n napari-cellulus python==3.9
+```
 
+2. Activate the newly-created environment:
 
+```
+conda activate napari-cellulus
+```
 
-To install latest development version :
+3a. If using a GPU, install pytorch cuda dependencies:
 
-    pip install git+https://github.com/funkelab/napari-cellulus.git
+```bash
+conda install pytorch==2.0.1 torchvision==0.15.2 pytorch-cuda=11.7 -c pytorch -c nvidia
+```
 
+3b. otherwise (if using a CPU or MPS), run:
 
-## Contributing
+```bash
+pip install torch torchvision
+```
 
-Contributions are very welcome. Tests can be run with [tox], please ensure
-the coverage at least stays the same before you submit a pull request.
+4. Install the package from github:
 
-## License
+```bash
+pip install git+https://github.com/funkelab/napari-cellulus.git
+```
 
-Distributed under the terms of the [MIT] license,
-"napari-cellulus" is free and open source software
+### Getting Started
 
-## Issues
+Run the following commands in a terminal window:
+```
+conda activate napari-cellulus
+napari
+```
 
-If you encounter any problems, please [file an issue] along with a detailed description.
+Next, select `Cellulus` from the `Plugins` drop-down menu.
 
-[napari]: https://github.com/napari/napari
-[Cookiecutter]: https://github.com/audreyr/cookiecutter
-[@napari]: https://github.com/napari
-[MIT]: http://opensource.org/licenses/MIT
-[BSD-3]: http://opensource.org/licenses/BSD-3-Clause
-[GNU GPL v3.0]: http://www.gnu.org/licenses/gpl-3.0.txt
-[GNU LGPL v3.0]: http://www.gnu.org/licenses/lgpl-3.0.txt
-[Apache Software License 2.0]: http://www.apache.org/licenses/LICENSE-2.0
-[Mozilla Public License 2.0]: https://www.mozilla.org/media/MPL/2.0/index.txt
-[cookiecutter-napari-plugin]: https://github.com/napari/cookiecutter-napari-plugin
+### Citation
 
-[file an issue]: https://github.com/funkelab/napari-cellulus/issues
+If you find our work useful in your research, please consider citing:
 
-[napari]: https://github.com/napari/napari
-[tox]: https://tox.readthedocs.io/en/latest/
-[pip]: https://pypi.org/project/pip/
-[PyPI]: https://pypi.org/
+
+```bibtex
+@misc{wolf2023unsupervised,
+      title={Unsupervised Learning of Object-Centric Embeddings for Cell Instance Segmentation in Microscopy Images},
+      author={Steffen Wolf and Manan Lalit and Henry Westmacott and Katie McDole and Jan Funke},
+      year={2023},
+      eprint={2310.08501},
+      archivePrefix={arXiv},
+      primaryClass={cs.LG}
+}
+```
+
+### Issues
+
+If you encounter any problems, please **[file an issue](https://github.com/funkelab/napari-cellulus/issues)** along with a description.

setup.cfg

@@ -5,9 +5,8 @@ description = A Napari plugin for Cellulus: Unsupervised Learning of Object-Cent
 long_description = file: README.md
 long_description_content_type = text/markdown
 url = https://github.com/funkelab/napari-cellulus
-author = William Patton
-author_email = [email protected]
-license = MIT
+author = William Patton, Manan Lalit
+author_email = [email protected], [email protected]
 license_files = LICENSE
 classifiers =
     Development Status :: 2 - Pre-Alpha
@@ -31,19 +30,16 @@ project_urls =
 [options]
 packages = find:
 install_requires =
-    numpy
-    magicgui
+    napari[all]
+    pyqtgraph
     qtpy
     cellulus @ git+https://github.com/funkelab/cellulus
-    matplotlib
-    torch
-    gunpowder
-
+    pre-commit
 
 python_requires = >=3.8
 include_package_data = True
 package_dir =
-    =src
+    = src
 
 # add your package requirements here
 

src/napari_cellulus/__init__.py

@@ -1,5 +1,5 @@
-__version__ = "0.0.3"
+__version__ = "0.1.0"
 
-from ._sample_data import tissuenet_sample
+from .sample_data import tissue_net_sample
 
-__all__ = ("tissuenet_sample",)
+__all__ = ("tissue_net_sample",)

src/napari_cellulus/meta_data.py → src/napari_cellulus/datasets/meta_data.py

@@ -11,7 +11,7 @@ def __init__(self, shape, axis_names):
         self.channel_dim = None
         self.time_dim = None
         self.spatial_array: Tuple[int, ...] = ()
-        self.spatial_dims = ()
+        self.spatial_dims: Tuple[int, ...] = ()
         for dim, axis_name in enumerate(axis_names):
             if axis_name == "s":
                 self.sample_dim = dim