[feat] docs: update docs

Author: bgallois

docs/user/installation.md

@@ -24,20 +24,20 @@ Stable versions of FastTrack are released for Linux (official makeself, official
         -   Download the FastTrack [installer FastTrackInstaller.exe](https://github.com/FastTrackOrg/FastTrack/releases/latest).
         -   Execute the installer and follow the provided instructions.
     * Portable:
-        - Download the FastTrack [folder FastTrack.zip] (https://github.com/FastTrackOrg/FastTrack/releases/latest).
+        - Download the FastTrack [folder FastTrack.zip](https://github.com/FastTrackOrg/FastTrack/releases/latest).
         - Unzip the folder and execute FastTrack.exe.
-2. For Linux (all distributions) as makeself:
-    * Download the AppImage [file FastTrack-x86_64.run](https://github.com/FastTrackOrg/FastTrack/releases/latest).
+2. For Linux (all distributions) as Makeself:
+    * Download the Makeself archive [FastTrack-x86_64.run](https://github.com/FastTrackOrg/FastTrack/releases/latest).
     * Allow FastTrack.run to be executed:
-        - Right-click on the AppImage file.
+        - Right-click on the run file.
         - Click on Properties.
         - Click on Permissions.
         - Tick “Allow executing file as program”.
 3. For Linux natively:
     * Arch Linux: `yay -S fasttrack fasttrack-cli`
     * From source : `mkdir build ; cd build ; cmake ../ ; make ; sudo make install`
 4.  For Mac (.app):
-    - Minimal version required based on Qt6 minimal version required.
+    - Minimal version required based on Qt6 supported minimal version.
     - Download the FastTrack dmg [FastTrack.dmg](https://github.com/FastTrackOrg/FastTrack/releases/latest).
     - Double click on the dmg file.
     - Drag the application from the dmg window into the Applications folder.
@@ -53,7 +53,7 @@ Follow these troubleshooting steps to ensure a seamless installation and optimal
 
 ### Application Authorization
 
-- **Unsigned Application Warning**: If you encounter a message stating that "FastTrack" is damaged and can't be opened, it's because the application is not signed and will not be signed ever.
+- **Unsigned Application Warning**: If you encounter a message stating that "FastTrack" is damaged and can't be opened, it's because the application is not signed with a valid Apple Developer ID.
   - **Solution**:
     1. Open the Terminal application.
 
@@ -93,7 +93,7 @@ FastTrack will display a message at the start-up and in the status bar when a ne
   Search the *FastTrackUpdater* in the *Windows Start Menu* or execute the *MaintenanceTool.exe* in the installation folder directly and follow the provided instructions.
 
 2. For Linux:  
-  The FastTrack AppImage does not currently support the automatic update. Replace the current AppImage with the latest AppImage released.
+  The FastTrack Makeself does not currently support the automatic update. Replace the current Makeself with the latest AppImage released.
 
 3. For Mac:  
     * The FastTrack App does not currently support the automatic update. Replace the current App with the latest App released.

docs/user/reference.md

@@ -10,13 +10,95 @@ sidebar_label: Reference
 
 ## Papers that cite FastTrack
 
-* [Golovkova, Iaroslava, et al. "Depletion attraction impairs the plasticity of emulsions flowing in a constriction." Soft Matter 16.13 (2020): 3294-3302.](http://www.dx.doi.org/10.1039/c9sm02343g)
-* [Candelier, Raphaël, et al. "A semi-automatic dispenser for solid and liquid food in aquatic facilities." Zebrafish 16.4 (2019): 401-407.](https://doi.org/10.1089/zeb.2019.1733)
-* [Goc, Guillaume Le, et al. "Thermal modulation of Zebrafish exploratory statistics reveals constraints on individual behavioral variability." BMC biology 19 (2021): 1-17.](https://hal.sorbonne-universite.fr/hal-03352907/document)
-* [Ray, Subhasis, and Mark A. Stopfer. "Argos: A toolkit for tracking multiple animals in complex visual environments." Methods in Ecology and Evolution (2021).](https://besjournals.onlinelibrary.wiley.com/doi/full/10.1111/2041-210X.13776?casa_token=Y7SmhKArnegAAAAA%3AQbUHTTQXDBFOPfCHoCKrCbZEfBF1SB1crGcFkIVcg8b9RT41PUQhpVRkALVE86HUs8N5MwrW6rkmE1s)
-* [Kamkar, Shiva, et al. "Brain-inspired multiple-target tracking using Dynamic Neural Fields." Neural Networks (2022).](https://www.sciencedirect.com/science/article/pii/S0893608022001046?casa_token=4gy8yPK2n1IAAAAA:SnLWd9dTHByclGcGSYYjb-zj62tM1MUdDHs0_SROYUFwIuunHAMvO_I7MkgSykLVUfcp2mQi)
-* [Bertram, Michael G., et al. "Frontiers in quantifying wildlife behavioural responses to chemical pollution." Biological Reviews (2022).](https://onlinelibrary.wiley.com/doi/full/10.1111/brv.12844)
-* [PREPRINT Kappel, Johannes M., et al. "Visual recognition of social signals by a tecto-thalamic neural circuit." bioRxiv (2021).](https://www.biorxiv.org/content/10.1101/2021.08.17.456614v1.abstract)
-* [PREPRINT Elices, Irene, et al. "An electrophysiological and behavioral model of Paramecium, the" swimming neuron"." bioRxiv (2022).](https://www.biorxiv.org/content/10.1101/2022.02.15.480485v1.abstract)
-* [PREPRINT Wolf, Sebastien, et al. "Emergence of time persistence in an interpretable data-driven neural network model." bioRxiv (2022).](https://www.biorxiv.org/content/10.1101/2022.02.02.478841v1.abstract)
+1. Experimental evidence of stress-induced critical state in schooling fish  
+   *G Lin, R Escobedo, X Li, T Xue, Z Han, C Sire, V Guttal…* - bioRxiv, 2025
 
+2. Quantitative Analysis of Biomolecular Condensates on a Modified Support  
+   *AS Shtork, II Pavlova, JI Svetlova, MS Iudin…* - Russian Journal of Bioorganic Chemistry, 2025
+
+3. Robot system for sequential suspending point selection, grasping, spreading, and aligning manipulation of randomly placed towel-like objects  
+   *T Wang, M Oka, K Murakami, S Huang, H Sumi…* - Robotics and Autonomous Systems, 2025
+
+4. The Role of PLAG1 in Brain Development  
+   *J Gasperoni* - La Trobe University, 2025
+
+5. Linking Brain and Behavior States in Zebrafish Larvae Locomotion using Hidden Markov Models  
+   *M Dommanget-Kott, J Fernandez-de-Cossio-Diaz…* - bioRxiv, 2024
+
+6. Structure and individuality of navigation in zebrafish larvae  
+   *M Dommanget-Kott, J Fernandez-De-Cossio-Diaz…* - Theses, 2024
+
+7. Investigating multiscale behavioral variability in larval zebrafish navigation  
+   *G Sridhar* - Theses, 2024
+
+8. Beyond observation: Deep learning for animal behavior and ecological conservation  
+   *LS Saoud, A Sultan, M Elmezain, M Heshmat…* - Ecological Informatics, 2024
+
+9. Philament: A filament tracking program to quickly and accurately analyze in vitro motility assays  
+   *RM Bowser, GP Farman, CC Gregorio* - Biophysical Reports, 2024
+
+10. Predicting the long-term collective behaviour of fish pairs with deep learning  
+    *V Papaspyros, R Escobedo, A Alahi…* - Journal of The Royal Society Interface, 2024
+
+11. Magnetic actuation of otoliths allows behavioral and brain-wide neuronal exploration of vestibulo-motor processing in larval zebrafish  
+    *N Beiza-Canelo, H Moulle, T Pujol, T Panier, G Migault…* - Current Biology, 2023
+
+12. A biohybrid interaction framework for the integration of robots in animal societies  
+    *V Papaspyros, D Burnier, R Cherfan, G Theraulaz…* - IEEE Transactions on Robotics, 2023
+
+13. Illuminance-tuned collective motion in fish  
+    *B Lafoux, J Moscatelli, R Godoy-Diana…* - Communications Biology, 2023
+
+14. Tuning social interactions' strength drives collective response to light intensity in schooling fish  
+    *T Xue, X Li, GZ Lin, R Escobedo, Z Han…* - PLoS Computational Biology, 2023
+
+15. Functional and mechanistic diversity in ant tandem communication  
+    *N Mizumoto, Y Tanaka, G Valentini, TO Richardson…* - IScience, 2023
+
+16. An electrophysiological and kinematic model of Paramecium, the “swimming neuron”  
+    *I Elices, A Kulkarni, N Escoubet…* - PLoS Computational Biology, 2023
+
+17. Toward Real-Time Animal Tracking with Integrated Stimulus Control for Automated Conditioning in Aquatic Eco-Neurotoxicology  
+    *Y Bai, J Henry, E Cheng, S Perry…* - Environmental Science & Technology, 2023
+
+18. Multi-Object Tracking in Heterogeneous environments (MOTHe) for animal video recordings  
+    *A Rathore, A Sharma, S Shah, N Sharma, C Torney…* - PeerJ, 2023
+
+19. Interaction of the mechanosensitive microswimmer Paramecium with obstacles  
+    *N Escoubet, R Brette, LL Pontani…* - Royal Society Open Science, 2023
+
+20. Protocol to obtain long movement trajectories of leaders and followers in ant tandem runs  
+    *Y Tanaka, G Valentini, SC Pratt, H Shimoji, N Mizumoto* - STAR Protocols, 2023
+
+21. A review of open-source image analysis tools for mammalian cell culture: algorithms, features and implementations  
+    *H Malik, AS Idris, SF Toha, IM Idris, MF Daud…* - PeerJ Computer Science, 2023
+
+22. Emergence of time persistence in a data-driven neural network model  
+    *S Wolf, G Le Goc, G Debrégeas, S Cocco, R Monasson* - Elife, 2023
+
+23. Predicting long-term collective animal behavior with deep learning  
+    *V Papaspyros, R Escobedo, A Alahi, G Theraulaz…* - bioRxiv, 2023
+
+24. A scalable assay for chemical preference of small freshwater fish  
+    *B Gallois, LL Pontani, G Debrégeas…* - Frontiers in Behavioral Neuroscience, 2022
+
+25. Frontiers in quantifying wildlife behavioural responses to chemical pollution  
+    *MG Bertram, JM Martin, ES McCallum…* - Biological Reviews, 2022
+
+26. Visual recognition of social signals by a tectothalamic neural circuit  
+    *JM Kappel, D Förster, K Slangewal, I Shainer, F Svara…* - Nature, 2022
+
+27. Argos: A toolkit for tracking multiple animals in complex visual environments  
+    *S Ray, MA Stopfer* - Methods in Ecology and Evolution, 2022
+
+28. Brain-inspired multiple-target tracking using dynamic neural fields  
+    *S Kamkar, HA Moghaddam, R Lashgari, W Erlhagen* - Neural Networks, 2022
+
+29. An early midbrain sensorimotor pathway is involved in the timely initiation and direction of swimming in the hatchling Xenopus laevis tadpole  
+    *MC Larbi, G Messa, H Jalal, S Koutsikou* - Frontiers in Neural Circuits, 2022
+
+30. Emergence of time persistence in an interpretable data-driven neural network model  
+    *S Wolf, GL Goc, S Cocco, G Debrégeas, R Monasson* - bioRxiv, 2022
+
+31. Thermal modulation of Zebrafish exploratory statistics reveals constraints on individual behavioral variability  
+    *GL Goc, J Lafaye, S Karpenko, V Bormuth, R Candelier…* - BMC Biology, 2021