Merge pull request #31 from volume-em/v1.1

V1.1 release

.gitignore

@@ -0,0 +1,160 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/

README.md

@@ -1,10 +1,24 @@
 # empanada-napari
 
-**The preprint describing this work is now available [on bioRxiv](https://www.biorxiv.org/content/10.1101/2022.03.17.484806v1).**
+> [!IMPORTANT]
+> **New Version Announcement!**
+> * New modules 
+>   * Morph labels - applies morphological operations to labels
+>   * Count labels - counts and lists the label IDs within the dataset
+>   * Filter labels - removes small pixel/voxel area labels or labels touching the image boundaries
+>   * Export and import a model - export or import locally saved model files to use within empanada-napari
+> * Updated modules 
+>   * Export segmentations - now allows 3D segmentations to be exported as a single .tiff image
+>   * Pick and save finetune/training patches - now allows paired grayscale and label mask images to create training patches 
+>   * Split label - now allows users to specify new label IDs 
+> * Updated documentation
+>   * Check out the updated documentation [here](https://empanada.readthedocs.io/en/latest/index.html)!
+
+**The paper describing this work is now available [on Cell Systems](https://www.cell.com/cell-systems/fulltext/S2405-4712(22)00494-X).**
 
 **Documentation for the plugin, including more detailed installation instructions, can be found [here](https://empanada.readthedocs.io/en/latest/empanada-napari.html).**
 
-[empanada](https://github.com/volume-em/empanada) is a tool for deep learning-based panoptic segmentation of 2D and 3D electron microscopy images of cells.
+empanada is a tool for deep learning-based panoptic segmentation of 2D and 3D electron microscopy images of cells.
 This plugin allows the running of panoptic segmentation models trained in empanada within [napari](https://napari.org).
 For help with this plugin please open an [issue](https://github.com/volume-em/empanada-napari/issues), for issues with napari specifically
 raise an [issue here instead](https://github.com/napari/napari/issues).
@@ -20,11 +34,17 @@ Volume EM datasets for benchmarking mitochondrial instance segmentation are avai
 
 ## Installation
 
-It's recommended to have installed napari through [conda](https://docs.conda.io/en/latest/miniconda.html).
-Then to install this plugin:
+### New Users
+
+If you've previously installed and used conda, it's recommended (but optional) to create a new virtual 
+environment in order to avoid dependency conflicts. 
+
+empanada-napari works with python=3.9 or lower
+
+It's recommended to have installed napari through [conda](https://docs.conda.io/en/latest/miniconda.html). Then to install this plugin:
 
 ```shell
-pip install empanada-napari
+pip install empanada-napari==1.1.0
 ```
 
 Launch napari:
@@ -35,6 +55,23 @@ napari
 
 Look for empanada-napari under the "Plugins" menu.
 
+
+### Returning Users
+
+If you installed napari into a virtual environment as suggested in the original release documentation, 
+be sure to activate it and uninstall the old empanada-napari.
+
+```shell
+pip uninstall empanada-napari
+```
+
+Then install the newest version:
+
+```shell
+pip install empanada-napari==1.1.0
+```
+
+
 ![empanada](images/demo.gif)
 
 ## GPU Support
@@ -75,15 +112,19 @@ conda install pytorch cudatoolkit=11.3 -c pytorch
 If you use results generated by this plugin in a publication, please cite:
 
 ```bibtex
-@article {Conrad2022.03.17.484806,
-	author = {Conrad, Ryan and Narayan, Kedar},
-	title = {Instance segmentation of mitochondria in electron microscopy images with a generalist deep learning model},
-	elocation-id = {2022.03.17.484806},
-	year = {2022},
-	doi = {10.1101/2022.03.17.484806},
-	publisher = {Cold Spring Harbor Laboratory},
-	URL = {https://www.biorxiv.org/content/early/2022/03/18/2022.03.17.484806},
-	eprint = {https://www.biorxiv.org/content/early/2022/03/18/2022.03.17.484806.full.pdf},
-	journal = {bioRxiv}
+@article { Conrad2023,
+    author = {Conrad, Ryan and Narayan, Kedar},
+    title = {Instance segmentation of mitochondria in electron microscopy images with a generalist deep learning model trained on a diverse dataset},
+    journal = {Cell Systems},
+    year = {2023},
+    month = {Jan},
+    day = {18},
+    publisher = {Elsevier},
+    volume = {14},
+    number = {1},
+    pages = {58-71.e5},
+    issn = {2405-4712},
+    doi = {10.1016/j.cels.2022.12.006},
+    url = {https://doi.org/10.1016/j.cels.2022.12.006}
 }
 ```

empanada_napari/__init__.py

@@ -15,6 +15,7 @@
     find_next_available_label_widget
 )
 from ._export_batch_segs import export_batch_segs_widget
+from ._label_counter_widget import label_counter_widget
 
 __all__ = [
     'slice_dock_widget',
@@ -31,5 +32,6 @@
     'morph_labels_widget',
     'jump_to_label_widget',
     'find_next_available_label_widget',
-    'export_batch_segs_widget'
+    'export_batch_segs_widget',
+    'label_counter_widget'
 ]