Merge branch 'main' into development

.gitignore

@@ -78,6 +78,7 @@ venv*
 paper/paper.jats
 paper/paper.pdf
 paper/media
+paper/notes.md
 
 !tests/**/*.mp4
-!tests/**/*.csv
+!tests/**/*.csv

README.md

@@ -20,38 +20,21 @@ Additionally, our software can be extended to include new methods and algorithms
 - **Support For High Temporal Videos**: The human blink is fast, and JeFaPaTo is designed to handle it. JeFaPaTo can process videos with any FPS but with an extraction optimized for 240 FPS.
 - **Anywhere**: JeFaPaTo is a cross-platform tool that allows you to use it on Windows, Linux, and MacOS.
 
-## Get Started
+## Getting Started
 
-Ready to dive into the world of precise facial feature extraction and analysis? Give JeFaPaTo a try and experience the power of this tool for yourself! Download the latest version of JeFaPaTo for your operating system from the [releases page](https://github.com/cvjena/JeFaPaTo/releases/tag/v1.0.0) or the following links:
+Ready to dive into the world of precise facial feature extraction and analysis? Give JeFaPaTo a try and experience the power of this tool for yourself! Download the latest version of JeFaPaTo for your operating system from the [releases page](https://github.com/cvjena/JeFaPaTo/releases) or the following links:
 
 - [Windows 11](https://github.com/cvjena/JeFaPaTo/releases/latest/download/JeFaPaTo_windows.exe)
 - [Linux/Ubuntu 22.04](https://github.com/cvjena/JeFaPaTo/releases/latest//download/JeFaPaTo_linux)
 - [MacOS Universal2 v13+](https://github.com/cvjena/JeFaPaTo/releases/latest/download/JeFaPaTo_universal2.dmg)
 - [MacOS Intel v13+](https://github.com/cvjena/JeFaPaTo/releases/latest/download/JeFaPaTo_intel.dmg)
 - [MacOS Intel v10.15+](https://github.com/cvjena/JeFaPaTo/releases/latest/download/JeFaPaTo_intel_v10.dmg)
 
-If you want to install JeFaPaTo from source, please follow the instructions in the [installation guide](INSTALL.md).
+## Tutorials
 
-## How to use JeFaPaTo
-
-### Facial Features
-
-1. Start JeFaPaTo
-2. Select the video file or drag and drop it into the indicated area
-3. The face should be found automatically; if not, adjust the bounding box
-4. Select the facial features you want to analyze in the sidebar
-5. Press the play button to start the analysis
-
-### Blinking Detection
-
-1. Start JeFaPaTo
-2. Select the feature "Blinking Detection" in the top bar
-3. Drag and drop the `.csv` file containing the EAR-Score values into the indicated area
-   - you can also drag and drop the video file into the indicated area to jump to the corresponding frame
-4. Press the `Extract Blinks` buttons to extract the blinks (in a future version, the settings are not needed anymore)
-5. In the table, you now have the option to label the blinks
-6. Press `Summarize` to get a summary of the blink behavior
-7. Press `Export` to export the data in the appropriate format
+If you want to know more about how to use `JeFaPaTo`, please refer to the [Wiki Pages](https://github.com/cvjena/JeFaPaTo/wiki).
+There, you can find a custom installation guide and two tutorials, one for the facial feature extraction and another one for the eye blink extraction.
+Additionally, we list specific background information on the usage of the tool.
 
 ## Citing JeFaPaTo
 

paper/paper.bib

@@ -8,20 +8,14 @@ @article{soukupovaRealTimeEyeBlink2016
   url = {https://api.semanticscholar.org/CorpusID:35923299},
 }
 
-@misc{lugaresiMediaPipeFrameworkBuilding2019,
-  title = {{{MediaPipe}}: {{A Framework}} for {{Building Perception Pipelines}}},
-  shorttitle = {{{MediaPipe}}},
-  author = {Lugaresi, Camillo and Tang, Jiuqiang and Nash, Hadon and McClanahan, Chris and Uboweja, Esha and Hays, Michael and Zhang, Fan and Chang, Chuo-Ling and Yong, Ming Guang and Lee, Juhyun and Chang, Wan-Teh and Hua, Wei and Georg, Manfred and Grundmann, Matthias},
-  year = {2019},
-  month = jun,
-  number = {arXiv:1906.08172},
-  eprint = {1906.08172},
-  primaryclass = {cs},
-  publisher = {{arXiv}},
-  doi = {10.48550/arXiv.1906.08172},
-  archiveprefix = {arxiv},
+@inproceedings{lugaresiMediaPipeFrameworkBuilding2019,
+  title = {{{MediaPipe}}: {{A}} Framework for Perceiving and Processing Reality},
+  booktitle = {Third Workshop on Computer Vision for {{AR}}/{{VR}} at {{IEEE}} Computer Vision and Pattern Recognition ({{CVPR}}) 2019},
+  author = {Lugaresi, Camillo and Tang, Jiuqiang and Nash, Hadon and McClanahan, Chris and Uboweja, Esha and Hays, Michael and Zhang, Fan and Chang, Chuo-Ling and Yong, Ming and Lee, Juhyun and Chang, Wan-Teh and Hua, Wei and Georg, Manfred and Grundmann, Matthias},
+  year = {2019}
 }
 
+
 @article{kartynnikRealtimeFacialSurface2019a,
   title = {Real-Time {{Facial Surface Geometry}} from {{Monocular Video}} on {{Mobile GPUs}}},
   author = {Kartynnik, Yury and Ablavatski, Artsiom and Grishchenko, Ivan and Grundmann, Matthias},
@@ -103,4 +97,141 @@ @ARTICLE{otsu
   number={1},
   pages={62-66},
   doi={10.1109/TSMC.1979.4310076}
-}
+}
+
+@article{kwonHighspeedCameraCharacterization2013,
+  title = {High-Speed Camera Characterization of Voluntary Eye Blinking Kinematics},
+  author = {Kwon, Kyung-Ah and Shipley, Rebecca J. and Edirisinghe, Mohan and Ezra, Daniel G. and Rose, Geoff and Best, Serena M. and Cameron, Ruth E.},
+  year = {2013},
+  month = aug,
+  journal = {Journal of the Royal Society, Interface},
+  volume = {10},
+  number = {85},
+  pages = {20130227},
+  issn = {1742-5662},
+  doi = {10.1098/rsif.2013.0227},
+  langid = {english},
+  pmcid = {PMC4043155},
+  pmid = {23760297},
+}
+
+@article{vanderwerfBlinkRecoveryPatients2007,
+  title = {Blink {{Recovery}} in {{Patients}} with {{Bell}}'s {{Palsy}}: {{A Neurophysiological}} and {{Behavioral Longitudinal Study}}},
+  shorttitle = {Blink {{Recovery}} in {{Patients}} with {{Bell}}'s {{Palsy}}},
+  author = {VanderWerf, Frans and Reits, Dik and Smit, Albertine Ellen and Metselaar, Mick},
+  year = {2007},
+  month = jan,
+  journal = {Investigative Ophthalmology \& Visual Science},
+  volume = {48},
+  number = {1},
+  pages = {203--213},
+  issn = {1552-5783},
+  doi = {10.1167/iovs.06-0499},
+  urldate = {2024-04-16},
+}
+
+@article{nuuttilaDiagnosticAccuracyGlabellar2021,
+  title = {Diagnostic Accuracy of Glabellar Tap Sign for {{Parkinson}}'s Disease},
+  author = {Nuuttila, Simo and Eklund, Mikael and Joutsa, Juho and Jaakkola, Elina and M{\"a}kinen, Elina and Honkanen, Emma A. and Lindholm, Kari and Noponen, Tommi and Ihalainen, Toni and Murtom{\"a}ki, Kirsi and Nojonen, Tanja and Levo, Reeta and Mertsalmi, Tuomas and Scheperjans, Filip and Kaasinen, Valtteri},
+  year = {2021},
+  journal = {Journal of Neural Transmission},
+  volume = {128},
+  number = {11},
+  pages = {1655--1661},
+  issn = {0300-9564},
+  doi = {10.1007/s00702-021-02391-3},
+  urldate = {2024-04-16},
+}
+
+@article{vanderwerfEyelidMovementsBehavioral2003,
+  title = {Eyelid Movements: Behavioral Studies of Blinking in Humans under Different Stimulus Conditions},
+  shorttitle = {Eyelid Movements},
+  author = {VanderWerf, Frans and Brassinga, Peter and Reits, Dik and Aramideh, Majid and {Ongerboer de Visser}, Bram},
+  year = {2003},
+  month = may,
+  journal = {Journal of Neurophysiology},
+  volume = {89},
+  number = {5},
+  pages = {2784--2796},
+  issn = {0022-3077},
+  langid = {english},
+}
+
+@article{cruzSpontaneousEyeblinkActivity2011,
+  title = {Spontaneous Eyeblink Activity},
+  author = {Cruz, Antonio A. V. and Garcia, Denny M. and Pinto, Carolina T. and Cechetti, Sheila P.},
+  year = {2011},
+  month = jan,
+  journal = {The Ocular Surface},
+  volume = {9},
+  number = {1},
+  pages = {29--41},
+  issn = {1542-0124},
+  langid = {english},
+  pmid = {21338567},
+}
+
+@article{volkInitialSeverityMotor2017,
+  title = {Initial Severity of Motor and Non-Motor Disabilities in Patients with Facial Palsy: An Assessment Using Patient-Reported Outcome Measures},
+  shorttitle = {Initial Severity of Motor and Non-Motor Disabilities in Patients with Facial Palsy},
+  author = {Volk, Gerd Fabian and Granitzka, Thordis and Kreysa, Helene and Klingner, Carsten M. and {Guntinas-Lichius}, Orlando},
+  year = {2017},
+  month = jan,
+  journal = {European archives of oto-rhino-laryngology: official journal of the European Federation of Oto-Rhino-Laryngological Societies (EUFOS): affiliated with the German Society for Oto-Rhino-Laryngology - Head and Neck Surgery},
+  volume = {274},
+  number = {1},
+  pages = {45--52},
+  issn = {1434-4726},
+  doi = {10.1007/s00405-016-4018-1},
+  abstract = {Patients with facial palsy (FP) not only suffer from their facial movement disorder, but also from social and psychological disabilities. These can be assessed by patient-reported outcome measures (PROMs) like the quality-of-life Short-Form 36 Item Questionnaire (SF36) or FP-specific instruments like the Facial Clinimetric Evaluation Scale (FaCE) or the Facial Disability Index (FDI). Not much is known about factors influencing PROMs in patients with FP. We identified predictors for baseline SF36, FaCE, and FDI scoring in 256 patients with unilateral peripheral FP using univariate correlation and multivariate linear regression analyses. Mean age was 52~{\textpm}~18~years. 153 patients (60~\%) were female. 90 patients (31~\%) and 176 patients (69~\%) were first seen {$<$}90 or {$>$}90~days after onset, respectively, i.e., with acute or chronic FP. House-Brackmann grading was 3.9~{\textpm}~1.4. FaCE subscores varied from 41~{\textpm}~28 to 71~{\textpm}~26, FDI scores from 65~{\textpm}~20 to 70~{\textpm}~22, and SF36 domains from 52~{\textpm}~20 to 80~{\textpm}~24. Older age, female gender, higher House-Brackmann grading, and initial assessment {$>$}90~days after onset were independent predictors for lower FaCE subscores and partly for lower FDI subscores (all p~{$<~$}0.05). Older age and female gender were best predictors for lower results in SF36 domains. Comorbidity was associated with lower SF General health perception and lower SF36 Emotional role (all p~{$<~$}0.05). Specific PROMs reveal that older and female patients and patients with chronic FP suffer particularly from motor and non-motor disabilities related to FP. Comorbidity unrelated to the FP could additionally impact the quality of life of patients with FP.},
+  langid = {english},
+  pmid = {27040558},
+  keywords = {Bell's palsy,Disability Evaluation,Disabled Persons,Facial nerve,Facial nerve reconstruction,Facial Paralysis,Humans,Patient Reported Outcome Measures,Patient-oriented methods,Quality of life,Quality of Life,Surveys and Questionnaires}
+}
+
+@article{louReviewAutomatedFacial2020,
+  title = {A {{Review}} on {{Automated Facial Nerve Function Assessment From Visual Face Capture}}},
+  author = {Lou, Jianwen and Yu, Hui and Wang, Fei-Yue},
+  year = {2020},
+  month = feb,
+  journal = {IEEE Transactions on Neural Systems and Rehabilitation Engineering},
+  volume = {28},
+  number = {2},
+  pages = {488--497},
+  issn = {1558-0210},
+  doi = {10.1109/TNSRE.2019.2961244},
+}
+
+@article{hochreiterMachineLearningBasedDetectingEyelid2023,
+  title = {Machine-{{Learning-Based Detecting}} of {{Eyelid Closure}} and {{Smiling Using Surface Electromyography}} of {{Auricular Muscles}} in {{Patients}} with {{Postparalytic Facial Synkinesis}}: {{A Feasibility Study}}},
+  shorttitle = {Machine-{{Learning-Based Detecting}} of {{Eyelid Closure}} and {{Smiling Using Surface Electromyography}} of {{Auricular Muscles}} in {{Patients}} with {{Postparalytic Facial Synkinesis}}},
+  author = {Hochreiter, Jakob and Hoche, Eric and Janik, Luisa and Volk, Gerd Fabian and Leistritz, Lutz and Anders, Christoph and {Guntinas-Lichius}, Orlando},
+  year = {2023},
+  month = jan,
+  journal = {Diagnostics},
+  volume = {13},
+  number = {3},
+  pages = {554},
+  publisher = {Multidisciplinary Digital Publishing Institute},
+  issn = {2075-4418},
+  doi = {10.3390/diagnostics13030554},
+  urldate = {2023-03-15},
+  langid = {english},
+}
+
+@article{chenSmartphoneBasedArtificialIntelligenceAssisted2021,
+  title = {Smartphone-{{Based Artificial Intelligence-Assisted Prediction}} for {{Eyelid Measurements}}: {{Algorithm Development}} and {{Observational Validation Study}}},
+  shorttitle = {Smartphone-{{Based Artificial Intelligence-Assisted Prediction}} for {{Eyelid Measurements}}},
+  author = {Chen, Hung-Chang and Tzeng, Shin-Shi and Hsiao, Yen-Chang and Chen, Ruei-Feng and Hung, Erh-Chien and Lee, Oscar K.},
+  year = {2021},
+  month = oct,
+  journal = {JMIR mHealth and uHealth},
+  volume = {9},
+  number = {10},
+  pages = {e32444},
+  issn = {2291-5222},
+  doi = {10.2196/32444},
+  langid = {english},
+  pmcid = {PMC8538024},
+  pmid = {34538776},
+}