Merge pull request #3 from datajoint/main

pull from upstream

.vscode/settings.json

@@ -4,9 +4,9 @@
     "editor.rulers": [
         88
     ],
-    "python.formatting.provider": "black",
+    "python.formatting.provider": "none",
     "[python]": {
-        "editor.defaultFormatter": null
+        "editor.defaultFormatter": "ms-python.black-formatter"
     },
     "[markdown]": {
         "editor.defaultFormatter": "disable"

CHANGELOG.md

@@ -3,6 +3,19 @@
 Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and
 [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) convention.
 
+## [0.9.2] - 2024-01-10
+
++ Fix - Imports and attribute values in notebooks to resolve DataJoint errors
+
+## [0.9.1] - 2023-12-19
+
++ Update - Tutorial notebook
++ Fix - minor fixes in `setup.py` and `README`
+
+## [0.9.0] - 2023-10-13
+
++ Add - Export to NWB and upload to DANDI
+
 ## [0.8.1] - 2023-08-31
 
 + Fix - Rename `get_image_files` to `get_calcium_imaging_files` where missed
@@ -177,6 +190,9 @@ Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and
 + Add - `scan` and `imaging` modules
 + Add - Readers for `ScanImage`, `ScanBox`, `Suite2p`, `CaImAn`
 
+[0.9.2]: https://github.com/datajoint/element-calcium-imaging/releases/tag/0.9.2
+[0.9.1]: https://github.com/datajoint/element-calcium-imaging/releases/tag/0.9.1
+[0.9.0]: https://github.com/datajoint/element-calcium-imaging/releases/tag/0.9.0
 [0.8.1]: https://github.com/datajoint/element-calcium-imaging/releases/tag/0.8.1
 [0.8.0]: https://github.com/datajoint/element-calcium-imaging/releases/tag/0.8.0
 [0.7.9]: https://github.com/datajoint/element-calcium-imaging/releases/tag/0.7.9

CONTRIBUTING.md

@@ -1,5 +1,5 @@
 # Contribution Guidelines
 
 This project follows the
-[DataJoint Contribution Guidelines](https://datajoint.com/docs/community/contribute/).
+[DataJoint Contribution Guidelines](https://datajoint.com/docs/about/contribute/).
 Please reference the link for more full details.

README.md

@@ -35,7 +35,7 @@ documentation page.
 + Clone the repository to your computer
 
   ```bash
-  git clone https://github.com/<enter_github_username>/element-calcium-imaging
+  git clone https://github.com/<enter_github_username>/element-calcium-imaging.git
   ```
 
 + Install with `pip`

docs/.docker/pip_requirements.txt

@@ -1,4 +1,4 @@
-mkdocs-material
+mkdocs-material==9.1.17
 mkdocs-redirects
 mkdocstrings
 mkdocstrings-python

docs/src/.overrides/assets/stylesheets/extra.css

@@ -96,7 +96,6 @@ html a[title="YouTube"].md-social__link svg {
     /* --md-footer-fg-color: var(--dj-white); */
 }
 
-[data-md-color-scheme="slate"] td,
-th {
+[data-md-color-scheme="slate"] .jupyter-wrapper .Table Td {
     color: var(--dj-black)
 }

docs/src/concepts.md

@@ -60,3 +60,18 @@ segmented.
 - Scanbox
 - Nikon NIS-Elements
 - Bruker Prairie View
+
+## Data Export and Publishing
+
+Element Calcium Imaging supports exporting of all data into standard Neurodata
+Without Borders (NWB) files. This makes it easy to share files with collaborators and
+publish results on [DANDI Archive](https://dandiarchive.org/).
+[NWB](https://www.nwb.org/), as an organization, is dedicated to standardizing data
+formats and maximizing interoperability across tools for neurophysiology.
+
+To use the export functionality with additional related dependencies, install the
+Element with the `nwb` option as follows:
+
+```console
+pip install element-calcium-imaging[nwb]
+```

docs/src/roadmap.md

@@ -16,8 +16,8 @@ the common motifs to create Element Calcium Imaging. Major features include:
 - [x] Quality metrics
 - [ ] Data compression
 - [ ] Deepinterpolation
-- [ ] Data export to NWB
-- [ ] Data publishing to DANDI
+- [x] Data export to NWB
+- [x] Data publishing to DANDI
 
 Further development of this Element is community driven. Upon user requests and based on
 guidance from the Scientific Steering Group we will continue adding features to this 

element_calcium_imaging/export/nwb/__init__.py

@@ -0,0 +1 @@
+from .nwb import imaging_session_to_nwb, write_nwb