Updated existing slides (#15)

* Updated existing slides * add jinja2 constraint * refactored out sections into separate .qmd files * updated feedback link * renamed notebook requirements file * fix typo in slides/SLEAP.qmd Co-authored-by: Chang Huan Lo <[email protected]> * fix typo in image * removed unnecessary image * make long list scrollable --------- Co-authored-by: Chang Huan Lo <[email protected]>
neuroinformatics-unit · Sep 30, 2024 · a29f5ac · a29f5ac
1 parent dbe027b
commit a29f5ac
Show file tree

Hide file tree

Showing 53 changed files with 7,091 additions and 601 deletions.
diff --git a/.github/workflows/render_and_deploy.yml b/.github/workflows/render_and_deploy.yml
@@ -45,6 +45,7 @@ jobs:
           mv index_files build/
           touch build/.nojekyll
           cp -r img build/
+          cp -r data build/
 
       - name: Deploy
         if: github.event_name == 'push' && github.ref_type == 'tag'

diff --git a/data/crab_ethogram_behaviours_Sanna.csv b/data/crab_ethogram_behaviours_Sanna.csv
@@ -0,0 +1,24 @@
+Parent category,Instantaneous behaviour,definition,,,
+locomotion,foraging, Foraging for detritus and small organisms on mudflats or in shallow waters. Dactyl(s) is moving towards the mouth. ,,,
+resting,burrowing, The crab is observed resting in its burrow. There are no conspecific interactions. ,,,
+locomotion?,entering burrow, Actively entering an uninhabited burrow.,,,
+locomotion?,exiting burrow, Actively exiting a burrow.,,,
+locomotion?,maintaining burrow," Digging and excavating burrows, carrying sediment to/from the burrow entrance. ",,,
+resting? ,protecting burrow," Standing over the entrance of a burrow, territorially (physical contact is a threat encounter). There do not have to be other crabs present to exhibit this behaviour; essentially, the crab is resting over the burrow entrance, usually with the dominant claw extended. ",,,
+conspecific aggression,attacking burrow, An intruder crab is forcefully removing a burrow resident by establishing physical contact - such as pereopod pulling. ,,,
+conspecific aggression,defending burrow,A burrow resident is being forcefully removed by an intruder via establishing physical contact - such as pereopod pulling. ,,,
+,threat display, Males may use their claws to intimidate rivals in territorial disputes (agonistic).,,,
+conspecific aggression,threat encounter,Physical contact among individuals (typically interlocking dominant claws) which does not occur above a burrow entrance. ,,,
+,waving, Males raise and wave their larger claw to attract females or communicate with other males.,,,
+,mating, Courtship rituals involving tactile contact. This includes mating (mounting) attempts. ,,,
+locomotion,walking, Walking or running on the mudbank. ,,,
+locomotion,swimming," The crab is fully submerged in the seawater. This includes remaining still (i.e., not ""swimming""), so long as the crab is entirely submerged. ",,,
+locomotion,entering seawater, Actively entering the seawater (not foraging). ,,,
+locomotion,exiting seawater, Actively exiting the seawater (not foraging). ,,,
+resting,mudbank resting," Resting on the mudbank (not in seawater or above a burrow). Often claws are positioned for protection, stabalisation, or the crab is cleaning it's eyestalks and maxillipeds.",,,
+resting,shoreline resting,"The crab is resting at the shoreline, where the waterline is approximately at mouth (maxilliped) height. The crab is not entirely submerged, foraging, nor exiting the seawater. Often claws are positioned for protection, stabalisation, or the crab is cleaning its eyestalks, maxillipeds, pereo- or pleopods.",,,
+,moulting, Shedding old exoskeleton in a process called molting to allow growth. ,,,
+locomotion,orientating,"Rotating the body in response to environmental cues, such as light and water levels, or a to protect the inhbitant's burrow against potential threat. This includes climbing up the crabitat wall to flip directions. ",,,
+resting,bubbling,"Expelling CO2 gas bubbles from gills during respiration, to reach homeostasis in a changing environment.",,,
+communication,tapping," Tapping on the substrate with (dominant) chelae, to vibrationally communicate with conspecifics.",,,
+,NV," Not visible. Husbandry records confirm this crab�s presence, but it was not visible at this observation interval. This crab was most likely burrowing at this time, although it may also have been entirely submerged in the seawater deep end (out of sight, and did not appear in-frame at any point throughout the observation period). ",,,
diff --git a/data/crab_ethogram_data_Sanna.csv b/data/crab_ethogram_data_Sanna.csv
@@ -0,0 +1,11 @@
+video file,season,day type,tide category,present population,present sex ratio,selected observation period start,real time,observation minute from start,crab ID,sex,instantaneous behaviour
+tub2023-04-23T08_00_00.avi,Spring,Weekend,high,25,21;4,20:34,20:35,1.00,52,m,shoreline resting
+tub2023-04-23T08_00_00.avi,Spring,Weekend,high,25,21;4,20:34,20:35,1.00,68,f,burrowing
+tub2023-04-23T08_00_00.avi,Spring,Weekend,high,25,21;4,20:34,20:36,2.00,52,m,shoreline resting
+tub2023-04-23T08_00_00.avi,Spring,Weekend,high,25,21;4,20:34,20:36,2.00,68,f,burrowing
+tub2023-04-23T08_00_00.avi,Spring,Weekend,high,25,21;4,20:34,20:37,3.00,52,m,shoreline resting
+tub2023-04-23T08_00_00.avi,Spring,Weekend,high,25,21;4,20:34,20:37,3.00,68,f,burrowing
+tub2023-04-23T08_00_00.avi,Spring,Weekend,high,25,21;4,20:34,20:38,4.00,52,m,shoreline resting
+tub2023-04-23T08_00_00.avi,Spring,Weekend,high,25,21;4,20:34,20:38,4.00,68,f,burrowing
+tub2023-04-23T08_00_00.avi,Spring,Weekend,high,25,21;4,20:34,20:39,5.00,52,m,swimming
+tub2023-04-23T08_00_00.avi,Spring,Weekend,high,25,21;4,20:34,20:39,5.00,68,f,burrowing
diff --git a/img/alessandro_felder.png b/img/alessandro_felder.png
diff --git a/img/array-jobs.svg b/img/array-jobs.svg
diff --git a/img/bg_logo_wide.png b/img/bg_logo_wide.png
diff --git a/img/empty-frame.png b/img/empty-frame.png
diff --git a/img/marr_three_levels.png b/img/marr_three_levels.png
diff --git a/img/mouse-annotated.png b/img/mouse-annotated.png
diff --git a/img/mouse-appearance-based-tracking.png b/img/mouse-appearance-based-tracking.png
diff --git a/img/mouse-bbox-tracking-multi-animal.png b/img/mouse-bbox-tracking-multi-animal.png
diff --git a/img/mouse-bbox-tracking-single-animal.png b/img/mouse-bbox-tracking-single-animal.png
diff --git a/img/mouse-bbox-tracking.png b/img/mouse-bbox-tracking.png
diff --git a/img/mouse-bbox.png b/img/mouse-bbox.png
diff --git a/img/mouse-centroid-tracking-multi-animal.png b/img/mouse-centroid-tracking-multi-animal.png
diff --git a/img/mouse-centroid-tracking-single-animal.png b/img/mouse-centroid-tracking-single-animal.png
diff --git a/img/mouse-centroid-tracking.png b/img/mouse-centroid-tracking.png
diff --git a/img/mouse-centroid.png b/img/mouse-centroid.png
diff --git a/img/mouse-ellipse-tracking.png b/img/mouse-ellipse-tracking.png
diff --git a/img/mouse-ellipse.png b/img/mouse-ellipse.png
diff --git a/img/mouse-frame.png b/img/mouse-frame.png
diff --git a/img/mouse-identity-tracking.png b/img/mouse-identity-tracking.png
diff --git a/img/mouse-mask.png b/img/mouse-mask.png
diff --git a/img/mouse-motion-based-tracking.png b/img/mouse-motion-based-tracking.png
diff --git a/img/mouse-multi-animal-keypoints.png b/img/mouse-multi-animal-keypoints.png
diff --git a/img/mouse-part-grouping.png b/img/mouse-part-grouping.png
diff --git a/img/mouse-pose-estimation.png b/img/mouse-pose-estimation.png
diff --git a/img/mouse-pose-tracking-multi-animal.png b/img/mouse-pose-tracking-multi-animal.png
diff --git a/img/mouse-pose-tracking-single-animal.png b/img/mouse-pose-tracking-single-animal.png
diff --git a/img/movement-dataset-multi-individual.png b/img/movement-dataset-multi-individual.png
diff --git a/img/movement-dataset-single-individual.png b/img/movement-dataset-single-individual.png
diff --git a/img/movement-repo-screenshot.png b/img/movement-repo-screenshot.png
diff --git a/img/movement_bboxes_dataset.png b/img/movement_bboxes_dataset.png
diff --git a/img/movement_bboxes_schematic.png b/img/movement_bboxes_schematic.png
diff --git a/img/movement_overview.png b/img/movement_overview.png
diff --git a/img/movement_poses_dataset.png b/img/movement_poses_dataset.png
diff --git a/img/movement_poses_schematic.png b/img/movement_poses_schematic.png
diff --git a/img/neuro_behav_mappings.png b/img/neuro_behav_mappings.png
diff --git a/img/open-source-tools-fig1b.png b/img/open-source-tools-fig1b.png
diff --git a/img/open-source-tools-fig2a.png b/img/open-source-tools-fig2a.png
diff --git a/img/sofia_minano.png b/img/sofia_minano.png
diff --git a/img/tracking_types.png b/img/tracking_types.png