Merge pull request #139 from bahanonu/bahanonu/functionUpdates

Update README, docs, license, and example data
bahanonu · Mar 20, 2024 · c168e84 · c168e84
2 parents 89fc0f8 + 4ce5a7a
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diff --git a/LICENSE b/LICENSE
@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (C) 2013-2021 Biafra Ahanonu
+Copyright (C) 2013-2024 Biafra Ahanonu
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/README.md b/README.md
@@ -23,6 +23,8 @@
 
 ## Full documentation at https://bahanonu.github.io/ciatah/.
 
+- Documentation for spinal cord motion correction can be found at https://bahanonu.github.io/ciatah/pipeline_detailed_spinal.
+
 Below are recordings and additional documents for users who want to learn more about calcium imaging analysis/experiments and the CIAtah pipeline.
 
 <ins> __Book chapter__ </ins> — We have a book chapter that goes over all steps of miniscope imaging: viral injections, GRIN lens probe implant, pain experimental design, data processing and neural/behavioral analysis, and more.
@@ -288,6 +290,19 @@ Please cite the [Ahanonu and Corder, 2022](https://doi.org/10.1007/978-1-0716-20
 }
 ```
 
+Please cite the [Ahanonu*, Crowther*, 2023](https://doi.org/10.1101/2023.05.22.541477) preprint on spinal cord imaging if you use related methods or procedures.
+
+```bibtex
+@article{ahanonu2023long,
+  title={Long-term optical imaging of the spinal cord in awake, behaving animals},
+  author={Ahanonu, Biafra and Crowther, Andrew and Kania, Artur and Casillas, Mariela Rosa and Basbaum, Allan},
+  journal={bioRxiv},
+  pages={2023--05},
+  year={2023},
+  publisher={Cold Spring Harbor Laboratory}
+}
+```
+
 Please see https://bahanonu.github.io/ciatah/references/ for additional references depending on processing steps undertaken.
 
 <!-- 

diff --git a/data/displacementFields/dots_reference.tif b/data/displacementFields/dots_reference.tif
diff --git a/data/displacementFields/dots_template.tif b/data/displacementFields/dots_template.tif
diff --git a/data/displacementFields/spinalImaging01_ref.tif b/data/displacementFields/spinalImaging01_ref.tif
diff --git a/data/displacementFields/spinalImaging01_template.tif b/data/displacementFields/spinalImaging01_template.tif
diff --git a/data/displacementFields/testFace_ref.jpg b/data/displacementFields/testFace_ref.jpg
diff --git a/data/displacementFields/testFace_template.jpg b/data/displacementFields/testFace_template.jpg
diff --git a/docs/docs/img/LD-MCM_DLCtrain_featureExclude.png b/docs/docs/img/LD-MCM_DLCtrain_featureExclude.png
diff --git a/docs/docs/img/LD-MCM_DeepLabCut_Annotation01.png b/docs/docs/img/LD-MCM_DeepLabCut_Annotation01.png
diff --git a/docs/docs/img/displacementFields_2p_data01.gif b/docs/docs/img/displacementFields_2p_data01.gif
diff --git a/docs/docs/img/displacementFields_2p_data02.png b/docs/docs/img/displacementFields_2p_data02.png
diff --git a/docs/docs/img/displacementFields_2p_manualGUI.png b/docs/docs/img/displacementFields_2p_manualGUI.png
diff --git a/docs/docs/img/modelPreprocessMovie_mcMethod_imregdemons01.png b/docs/docs/img/modelPreprocessMovie_mcMethod_imregdemons01.png
diff --git a/docs/docs/img/spinalFixed_runningWheel.png b/docs/docs/img/spinalFixed_runningWheel.png
diff --git a/docs/docs/index.md b/docs/docs/index.md
@@ -5,8 +5,7 @@
 [![GitHub release (latest by date)](https://img.shields.io/github/v/release/bahanonu/calciumImagingAnalysis?style=flat-square&logo=appveyor)](https://github.com/bahanonu/calciumImagingAnalysis/releases/latest?style=flat-square&logo=appveyor)
 ![GitHub code size in bytes](https://img.shields.io/github/languages/code-size/bahanonu/calciumImagingAnalysis?style=flat-square&logo=appveyor)
 [![Maintenance](https://img.shields.io/badge/Maintained%3F-yes-green.svg?style=flat-square)](https://github.com/bahanonu/calciumImagingAnalysis/graphs/commit-activity?style=flat-square&logo=appveyor)
-![visitors](https://visitor-badge.glitch.me/badge?page_id=bahanonu.calciumImagingAnalysis)
-![Hits](https://hitcounter.pythonanywhere.com/count/tag.svg?url=https%3A%2F%2Fgithub.com%2Fbahanonu%2FcalciumImagingAnalysis)
+![visitors](https://vbr.wocr.tk/badge?page_id=bahanonu.ciatah)
 
 <img src="https://user-images.githubusercontent.com/5241605/51068051-78c27680-15cd-11e9-9434-9d181b00ef8e.png" align="center">
 
@@ -29,15 +28,41 @@ __Download the software at [https://github.com/bahanonu/ciatah](https://github.c
 
 ## Guides
 
-Below are recordings for users who want to learn more about calcium imaging analysis.
+<!-- Below are recordings for users who want to learn more about calcium imaging analysis.
 
 - Read my overview of calcium imaging analysis methods at [Calcium imaging cell identification and fluorescence activity trace reconstruction, part 1](https://bahanonu.com/brain/#c20181209).
 
 ### Webinar
 This webinar gives an overview of calcium imaging analysis (with a focus on CIAtah) along with tips for improving experiments and analysis: https://info.inscopix.com/inscopix-inspire-view-webinarbiafra-ahanonu-signal-in-the-noise-distinguishing-relevant-neural-activity-in-calcium-imaging.
 
 ### Workshop tutorial
-This recording gives an overview of setting up and using CIAtah: https://www.youtube.com/watch?v=I6abW3uuJJw.
+This recording gives an overview of setting up and using CIAtah: https://www.youtube.com/watch?v=I6abW3uuJJw. -->
+
+Below are recordings and additional documents for users who want to learn more about calcium imaging analysis/experiments and the CIAtah pipeline.
+
+<ins> __Book chapter__ </ins> — We have a book chapter that goes over all steps of miniscope imaging: viral injections, GRIN lens probe implant, pain experimental design, data processing and neural/behavioral analysis, and more.
+
+- See [Ahanonu, B., Corder, G. (2022). _Recording Pain-Related Brain Activity in Behaving Animals Using Calcium Imaging and Miniature Microscopes_](https://doi.org/10.1007/978-1-0716-2039-7_13) (https://doi.org/10.1007/978-1-0716-2039-7_13).
+
+<ins>__Spinal cord motion correction methods__</ins> — Methods for motion correction of spinal imaging data using feature identification (e.g. with DeepLabCut), control point registration, and other methods. Additional updates will be integrated into CIAtah in the future.
+
+- Preprint: Ahanonu and Crowther, _et al_. (2023). _Long-term optical imaging of the spinal cord in awake, behaving animals_. bioRxiv (https://www.biorxiv.org/content/10.1101/2023.05.22.541477v1.full).
+
+<ins>__Webinars__</ins>
+
+- My INSCOPIX INSPIRE webinar gives an overview of calcium imaging analysis (with a focus on CIAtah) along with tips for improving experiments and analysis: "Signal in the noise: Distinguishing relevant neural activity in calcium imaging".
+
+  - https://info.inscopix.com/inscopix-inspire-view-webinarbiafra-ahanonu-signal-in-the-noise-distinguishing-relevant-neural-activity-in-calcium-imaging.
+
+- Our INSCOPIX INSIGHTS seminar describing awake and freely moving spinal cord imaging: "Long-term, multicolor spinal cord neural imaging in freely moving animals".
+
+  - https://info.inscopix.com/insights-webinar-view-biafra-ahanonu-andrew-crowther_long-term-multicolor-spinal-cord-neural-imaging-in-freely-moving-animals.
+
+<ins>__Workshop tutorial__</ins> — This recording gives an overview of setting up and using CIAtah: https://www.youtube.com/watch?v=I6abW3uuJJw.
+
+<ins>__Imaging analysis tools__</ins> My table with many current imaging analysis tools: https://github.com/bahanonu/imaging_tools.
+
+<ins>__GRINjector__</ins> — A surgical device to help with implanting gradient-refractive index (GRIN) lens probes into the brain or other regions: https://github.com/bahanonu/GRINjector.
 
 <!-- <img src="https://user-images.githubusercontent.com/5241605/94530890-9c3db280-01f0-11eb-99f0-e977f5edb304.gif" align="center" title="ciapkgMovie" alt="ciapkgMovie" width="75%" style="margin-left:auto;margin-right:auto;display:block;margin-bottom: 1%;">
  -->
@@ -110,6 +135,10 @@ Please [open an issue on GitHub](https://github.com/bahanonu/calciumImagingAnaly
 Made in USA.<br>
 <img src="https://user-images.githubusercontent.com/5241605/71493809-322a5400-27ff-11ea-9b2d-52ff20b5f332.png" align="center" title="USA" alt="USA" width="100px">
 
+## Repository stats
 - ![Hits](https://hitcounter.pythonanywhere.com/count/tag.svg?url=https%3A%2F%2Fgithub.com%2Fbahanonu%2FcalciumImagingAnalysis) (starting 2020.09.16)
 - ![visitors](https://visitor-badge.glitch.me/badge?page_id=bahanonu.calciumImagingAnalysis) (starting 2020.09.22)
+- ![visitors](https://visitor-badge.glitch.me/badge?page_id=bahanonu.calciumImagingAnalysis)
+- ![Hits](https://hitcounter.pythonanywhere.com/count/tag.svg?url=https%3A%2F%2Fgithub.com%2Fbahanonu%2FcalciumImagingAnalysis)
+- ![visitors](https://vbr.wocr.tk/badge?page_id=bahanonu.ciatah.docs) (starting 2023.06.12, specific to docs homepage)
 <!-- - [![HitCount](http://hits.dwyl.com/bahanonu/calciumImagingAnalysis.svg)](http://hits.dwyl.com/bahanonu/calciumImagingAnalysis) (starting 2020.08.16), frozen til `dwyl` migrates to new server. -->
diff --git a/docs/docs/pipeline_detailed_cross_session.md b/docs/docs/pipeline_detailed_cross_session.md
@@ -34,7 +34,7 @@ Below is an example of what that `globalIDs` matrix looks like when visualized.
 ## Notes on `computeMatchObjBtwnTrials` options
 
 After starting `computeMatchObjBtwnTrials`, the below options screen will appear:   
-<a href="https://user-images.githubusercontent.com/5241605/126746771-c0486ab8-aec1-429d-b982-88f638a400a8.png" target="_blank"><img src="https://user-images.githubusercontent.com/5241605/126746771-c0486ab8-aec1-429d-b982-88f638a400a8.png" alt="Cross session options screen" width="50%"/></a>
+<a href="https://user-images.githubusercontent.com/5241605/126746771-c0486ab8-aec1-429d-b982-88f638a400a8.png" target="_blank"><img src="https://user-images.githubusercontent.com/5241605/126746771-c0486ab8-aec1-429d-b982-88f638a400a8.png" alt="Cross session options screen" width="100%"/></a>
 
 An explanation of each option is as follows:
 

diff --git a/docs/docs/vid/thy1-gfp_day1-479.mp4 b/docs/docs/vid/thy1-gfp_day1-479.mp4
diff --git a/docs/mkdocs.yml b/docs/mkdocs.yml
@@ -75,6 +75,7 @@ nav:
   - End-to-end:
     # - One-page readme: alldocs.md
     - One-page readme: all_docs.md
+    - One-page readme (auto): all_docs.md
   - Setup:
     - Quick Start: install.md
     - Install: install_alt.md
@@ -88,6 +89,7 @@ nav:
     - Overview: pipeline_overview.md
     # - Step-by-step: pipeline_detailed.md
     - One-page step-by-step: pipeline_detailed_all.md
+    - One-page step-by-step (auto): pipeline_detailed.md
     - 1| Downsample raw movies: pipeline_detailed_downsample_raw.md
     - 2| Check pre-process settings: pipeline_detailed_preprocess_check.md
     - 3| <u><strong>Processing imaging movies</strong></u>: pipeline_detailed_preprocess.md
@@ -98,6 +100,8 @@ nav:
     - 8| <u><strong>Manual cell sorting</strong></u>: pipeline_detailed_signal_sorting_manual.md
     - 9| Region-specific analysis: pipeline_detailed_signal_region_analysis.md
     - 10| <u><strong>Cross-session alignment</strong></u>: pipeline_detailed_cross_session.md
+  - Spinal cord motion correction:
+    - Spinal cord motion correction: pipeline_detailed_spinal.md
   - Animal tracking:
     - Animal tracking (ImageJ+MATLAB): pipeline_animal_tracking.md
   - API: