ibs-lab · jccutler · Sep 6, 2024 · Sep 8, 2024 · Sep 8, 2024 · Sep 8, 2024
diff --git a/.gitignore b/.gitignore
@@ -167,6 +167,7 @@ src/cedalion/_version.py
 
 # rendered example notebooks
 docs/examples/*.ipynb
+docs/examples/*/*.ipynb
 
 # API documentation from sphinx-apidoc
 docs/api/*

diff --git a/CITATION.cff b/CITATION.cff
@@ -0,0 +1,9 @@
+cff-version: 1.2.0
+message: "If you use this software, please cite it as below."
+authors:
+- family-names: "Intelligent Biomedical Sensing (IBS) Lab"
+- family-names: "Cedalion Developers"
+title: "Cedalion Python Toolbox"
+version: 1.0.0
+date-released: 2024-09-08
+url: "https://github.com/ibs-lab/cedalion"
diff --git a/README.md b/README.md
@@ -16,6 +16,7 @@ well as several [example notebooks](https://doc.ibs.tu-berlin.de/cedalion/doc/de
 that illustrate the functionality of the toolbox.
 For discussions and help you can visit the [cedalion forum on openfnirs.org](https://openfnirs.org/community/cedalion/)
 
+
 ## Development environment
 
 To create a conda environment with the necessary dependencies run:
@@ -51,3 +52,7 @@ and then build the environment with the --solver=libmamba
 ```
 $ conda env create -n cedalion -f environment_dev.yml --solver=libmamba
 ```
+
+## How to cite Cedalion
+A paper for the toolbox is currently in the making. If you use this toolbox for a publication in the meantime, please cite us using GitHub's  "Cite this repository" feature in the "About" section. If you want to contact us or learn more about the IBS-Lab please go to https://www.ibs-lab.com/
+
diff --git a/docs/_static/IBS_Logo_sm.png b/docs/_static/IBS_Logo_sm.png
diff --git a/docs/community/contributing_code.md b/docs/community/contributing_code.md
@@ -4,6 +4,4 @@ This section is WIP.
 Here you will find information on how to interface your own developments with cedalion to facilitate contributing it to the toolbox to make it available to the broader community.
 In the meantime, you can find a small introduction to how to contribute code to cedalion below:
 
-```{toctree}
-contributing_code/contributing_code.md
-```
+[Getting Started with Contributing Code](https://doc.ibs.tu-berlin.de/cedalion/doc/dev/getting_started/contributing_code/contributing_code.html)
diff --git a/docs/community/contributors.md b/docs/community/contributors.md
@@ -2,7 +2,7 @@
 
 This section is WIP. You will find more information and detailed stats here soon. 
 
-Cedalion is an open source project driven by the [IBS-Lab](https://ibs-lab.com/) with the aim to encourage continuous use, contribution and improvement from the whole community to make it last. Therefore, code credit is important to us.
+Cedalion is an open source project driven by the [IBS-Lab](https://ibs-lab.com/) with the aim to encourage continuous use, contribution and improvement from the whole community to make it last. Therefore, it is important to us establish a transparent system of crediting contributors.
 
 
 ## Code Credit

diff --git a/docs/community/toolboxes.md b/docs/community/toolboxes.md
@@ -6,11 +6,11 @@ This section is WIP.
 
 A part of the core set of Cedalion's scientific fNIRS processing functionality is based on the matlab toolboxes [Homer2/3](https://github.com/BUNPC/Homer3) and [AtlasViewer](https://github.com/BUNPC/AtlasViewer) from which we have adopted methods into the python ecosystem.
 
-## Current toolboxes cedalion interfaces with:
+## Current toolboxes cedalion interfaces with
 - [Monte Carlo Xtreme](http://mcx.space/), for Monte-Carlo-based photon simulation
 - [NIRFASTer](https://github.com/nirfaster/NIRFASTer), for FEM-based photon simulation
 
-## Planned future toolboxes:
+## Planned future toolboxes
 - [MNE](https://mne.tools/stable/index.html), for state of the art EEG/MEG processing functionality
 - [NeuroKit](https://github.com/neuropsychology/NeuroKit), for Neurophysiological Signal Processing
 - [...?](https://openfnirs.org/software/)
diff --git a/docs/conf.py b/docs/conf.py
@@ -69,3 +69,8 @@
 
 # -- sphinx_autodoc_typehints -------------------------------------------------
 always_use_bars_union = True
+
+# -- Nbsphinx gallery ----------------------------------------------------------------
+nbsphinx_thumbnails = {
+    'examples/*/*': '_static/IBS_Logo_sm.png',
+}
diff --git a/docs/examples.rst b/docs/examples.rst
@@ -0,0 +1,62 @@
+Examples
+========
+
+.. contents::
+   :local:
+
+Getting Started and IO
+----------------------
+
+.. nbgallery::
+   :glob:
+
+   examples/getting_started_io/*
+
+Signal Quality
+-----------------------
+
+.. nbgallery::
+   :glob:
+
+   examples/signal_quality/*
+
+Modeling
+-----------------------
+
+.. nbgallery::
+   :glob:
+
+   examples/modeling/*
+
+Head Models and Image Reconstruction
+-------------------------------------
+
+.. nbgallery::
+   :glob:
+
+   examples/head_models/*
+
+Machine Learning and Data Driven Methods
+----------------------------------------
+
+.. nbgallery::
+   :glob:
+
+   examples/machine_learning/*
+
+Data Augmentation
+-----------------------
+
+.. nbgallery::
+   :caption: Coming soon
+   :glob:
+
+   examples/data_augmentation/*
+
+Plots & Visualization
+-----------------------
+
+.. nbgallery::
+   :glob:
+
+   examples/plots_visualization/*
diff --git a/docs/examples/Makefile b/docs/examples/Makefile
@@ -1,24 +1,25 @@
-EXAMPLE_NOTEBOOKS = xarray_datastructs_fnirs.ipynb \
-					finger_tapping_lda_classification.ipynb \
-					scalp_coupling_index.ipynb \
-					1010_system.ipynb \
-					image_reconstruction.ipynb \
-					store_hrfs_in_snirf_file.ipynb \
-					recording.ipynb \
-					glm_basis_functions.ipynb \
-					glm_illustrative_example.ipynb \
-					glm_fingertapping_example.ipynb 
-
-					#photogrammetric_optode_coregistration.ipynb \
-					#pruning_and_motion_artifacts.ipynb \
+EXAMPLE_NOTEBOOKS = getting_started_io/00_test_installation.ipynb \
+                    getting_started_io/10_xarray_datastructs_fnirs.ipynb \
+                    getting_started_io/11_recording_container.ipynb \
+					getting_started_io/13_data_structures_intro.ipynb \
+                    getting_started_io/34_store_hrfs_in_snirf_file.ipynb \
+                    plots_visualization/12_plots_example.ipynb \
+                    machine_learning/50_finger_tapping_lda_classification.ipynb \
+                    modeling/31_glm_basis_functions.ipynb \
+                    modeling/32_glm_fingertapping_example.ipynb \
+                    modeling/33_glm_illustrative_example.ipynb \
+                    signal_quality/20_scalp_coupling_index.ipynb \
+                    signal_quality/21_data_quality_and_pruning.ipynb \
+                    signal_quality/22_motion_artefacts_and_correction.ipynb \
+                    head_models/40_image_reconstruction.ipynb \
+                    head_models/41_photogrammetric_optode_coregistration.ipynb \
+                    head_models/42_1010_system.ipynb \
+                    head_models/43_crs_and_headmodel.ipynb
 
 .PHONY: notebooks
 
 notebooks: $(EXAMPLE_NOTEBOOKS)
 
-$(EXAMPLE_NOTEBOOKS) : %.ipynb : ../../examples/%.ipynb
+$(EXAMPLE_NOTEBOOKS): %.ipynb : ../../examples/%.ipynb
 	jupyter nbconvert --ExecutePreprocessor.store_widget_state=True --to notebook \
-	      --execute --output-dir=. $^
-
-clean:
-	rm -f $(EXAMPLE_NOTEBOOKS)
+	      --execute --output-dir=$(dir $@) $<
diff --git a/docs/examples/index.md b/docs/examples/index.md
diff --git a/docs/img/recording/dataarray_indexing_overview.png b/docs/img/recording/dataarray_indexing_overview.png
diff --git a/docs/img/recording/ndarray.png b/docs/img/recording/ndarray.png
diff --git a/docs/img/recording/rec_container_overview.png b/docs/img/recording/rec_container_overview.png
diff --git a/docs/index.md b/docs/index.md
@@ -1,18 +1,17 @@
 # Cedalion
 
-![cedalion graphical abstract](/docs/img/cedalion_frontpage.png)
+![cedalion graphical abstract](img/cedalion_frontpage.png)
 
 A python-based framework for the data driven analysis of multimodal fNIRS and DOT in naturalistic environments. Developed by the Intelligent Biomedical Sensing (IBS) Lab with and for the community.
 
 ```{toctree}
 :maxdepth: 1
 :caption: Contents
-:titlesonly:
 
 rationale.md
 getting_started/index.md
 data_structures/index.md
-examples/index.md
+examples
 community/index.md
 API <api/modules.rst>
 references.rst
@@ -21,7 +20,7 @@ LICENSE.md
 
 ## Special Thanks
 We cordially thank our friends and long-term collaborators at the BOAS Lab for their contributions and support in starting this project.
-![special thanks](/docs/img/special_thanks.png)
+![special thanks](img/special_thanks.png)
 
 ## Version
 This documentation was built from commit {{commit_hash}}.
diff --git a/docs/references.bib b/docs/references.bib
@@ -186,3 +186,17 @@ @misc{Luke2021
 year = {2021},
 url = {https://github.com/rob-luke/BIDS-NIRS-Tapping}
 }
+
+@article{Holmes1998,
+  title={Enhancement of MR Images Using Registration for Signal Averaging},
+  author={Holmes, Colin J. and Hoge, Rick and Collins, Louis and Woods, Roger and Toga, Arthur W. and Evans, Alan C.},
+  journal={Journal of Computer Assisted Tomography},
+  volume={22},
+  number={2},
+  pages={324--333},
+  year={1998},
+  month={March},
+  publisher={Lippincott Williams \& Wilkins},
+  url={https://journals.lww.com/jcat/abstract/1998/03000/enhancement_of_mr_images_using_registration_for.32.aspx},
+  doi={10.1097/00004728-199803000-00032}
+}