Updated use cases

UC1_AIBS.md

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+
+# Use Case 1 - Visual Change Detection (AIBS)
+
+## Key Personnel/Points of Contact
+
+* Marina Garrett
+* Doug Ollerenshaw
+
+
+## Metadata Focus Areas
+
+### Task : Image Change Detection
+
+This is a continuously-presented, flashed natural scene change detection
+task. For each trial, a natural image is presented for 250ms followed
+by 500ms of gray screen. On GO trials, a change in image identity
+occurs and mice must lick within the 750ms (one trial sequence)
+response window to receive a water reward.  On CATCH trials, no
+stimulus change occurs (same image presented again) and the behavioral
+response is measured to quantify guessing behavior. In addition, to
+test whether expectation signals were present in the visual cortex
+during this task, \~5\% of all non-change flashes were omitted; this
+corresponds to a gap in the regular timing of stimuli (was not done in
+all sessions). 
+
+Session structure:  Change-type was chosen based on predetermined
+frequencies; For the natural image phase in which there were 64
+change-pair possibilities (8 images in a set), CATCH frequency was set
+to 12.5% (1/8 of the total number of transitions). To ensure even
+sampling of all stimulus transitions, a transition path is selected
+at random from a matrix of 1000 pre-generated paths. Each path takes a
+pre-determined route through each of the 64 possible transitions,
+including same-to-same, or catch, transitions. 
+
+Behavior sessions across all phases began with 5 free-reward
+trials. To promote continued task engagement, a free reward was
+delivered after 10 consecutive MISS trials.
+
+Note: 'Trial' in this experiment refers to the occurrence of one
+'change' or 'omission' or 'catch' transition? I would say just flashed
+image+interstimulus interval, 
+
+Per session metadata:
+* duration (~1 hr)
+* image set (1 of 4)
+* etc... 
+
+Per trial metadata:
+* change type  (GO, CATCH)
+* change time (time/frame number)
+* next_image (image identity [0..7])
+* inter-change interval (time to next change)
+* etc...
+
+
+### Stimulus
+
+**Image sets:**
+* Modality: Visual
+* Stimulus type: Natural images
+* Variable parameters: Image identity
+* 1 familiar image set and 3 different novel image sets
+* Each image set is 8 natural images, for 32 images
+* One set of images shown per individual session
+* Images originated from 3 different databases of natural scene
+images:
+	1. the Berkeley Segmentation Dataset (images 000, 005, 012, 013,
+	024, 031, 034, 035, 036, 044, 047, 045, 054, 057) (Strasburger et
+	al., 2011),
+	2. the van Hateren Natural Image Dataset (images 061, 062, 063,
+	065, 066, 069, 072, 073, 075, 077, 078, 085, 087, 091) (van
+	Hateren and van der Schaaf, 1998)
+	3. the McGill Calibrated Colour Image Database (images 104, 106,
+	114, 115) (Olmos and Kingdom, 2004).
+* grayscale
+* contrast normalized (?)
+* matched to have equal mean luminance
+* Size: 1174 X 918 pixels
+
+**Device setup:**
+* Monitor: ASUS PA248Q LCD 
+* Screen resolution: 1920 x 1200 pixels
+* Mean screen luminance: 50 cd/m2
+* Viewing distance: 15 cm from the mouse’s eye (spanned 120 deg X 95 deg
+of visual space)
+* Monitor orientation: rotated 30° relative to the animal’s midline and
+tilted 70° off the horizon
+* Eye of presentation: monocular (ipsi? contra?)
+
+
+### Registration of spatial coordinates
+
+* Visual areas identified by intrinsic signal imaging (should document
+Marina's procedure? see ref)
+
+
+### Genotype/strain metadata
+
+* Male and female transgenic mice expressing GCaMP6f in:
+
+1. VIP inhibitory interneurons (double transgenic: VIP-IRES-Cre x
+Ai148 mice; https://www.jax.org/strain/010908,
+https://www.jax.org/strain/030328) or;
+
+2. Excitatory glutamatergic neurons (triple transgenic:
+   Slc17a7-IRES2-Cre x CaMKII-tTA x Ai93;
+   https://www.jax.org/strain/023527,
+   https://www.jax.org/strain/010712,
+   https://www.jax.org/strain/024108).
+
+
+
+## Questions/Next steps
+
+* How is the task transition matrix generated?
+* Distribution of times to next image change? How computed?
+* Talk to Marina about spatial registration for each unit? Are they
+  registering the visual area for each cell they image? Data was
+  pooled across areas, but should still have estimates
+* Were image sets always the same (i.e. did Set 1 have the same 8
+  images always for each animal? Or did each animal get different
+  configurations of the 32 for each set?
+
+
+
+## References
+
+1. Marina E. Garrett, Sahar Manavi, Kate Roll, Douglas
+    R. Ollerenshaw, Peter A. Groblewski, Justin Kiggins, Xiaoxuan Jia,
+    Linzy Casal, Kyla Mace, Ali Williford, Arielle Leon, Stefan
+    Mihalas, Shawn R. Olsen. (2019) Experience shapes activity
+    dynamics and stimulus coding of VIP inhibitory and excitatory
+    cells in visual cortex. bioRxiv 686063. doi: https://doi.org/10.1101/686063 
+
+2. Strasburger H, Rentschler I, Jüttner M. (2011) Peripheral vision
+   and pattern recognition: A review. J Vis
+   11:1–82. doi: https://doi.org/10.1167/11.5.13
+
+3. van Hateren JH, van der Schaaf A. (1998) Independent component
+   filters of natural images compared with simple cells in primary
+   visual cortex. Proc Biol Sci 265:359–366. doi:
+   https://doi.org/10.1098/rspb.1998.0303
+
+4. Olmos A, Kingdom FAA. (2004) A biologically inspired algorithm for
+   the recovery of shading and reflectance images. Perception
+   33:1463–1473. doi: https://doi.org/10.1068/p5321
+
+
+
+
+
+
+
+

UC2_MAP.md

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+
+# Use Case 2 - Motor Planning (Svoboda/MAP)
+
+## Key Personnel/Points of Contact
+
+* Karel Svoboda
+* Nuo Li
+
+
+## Metadata Focus Areas
+
+### Task: Tactile delayed response task
+
+The mouse must decide whether a metal pole is presented in an
+anterior or posterior position, and after a delay, must lick a left or
+right lickport with a water reward to indicate its choice. 
+
+1. A vertical pole moved into the plane within reach of the C2
+whisker (0.2 s travel time). The pole remained within reach for 1
+second, after which it was retracted. The retraction time was 0.2
+second, of which the pole remained within reach in the first 0.1
+second. The sample epoch is the time from onset of pole movement
+to 0.1 s after the retraction onset of the pole (sample epoch, 1.3 s total).
+
+2. The delay epoch lasted for another 1.2 seconds after the completion
+of pole retraction (delay epoch, 1.3 s total). An auditory \'response\'
+cue indicated the end of the delay epoch.
+
+3. Licking the correct lickport after the auditory response cue led
+to a small drop of liquid reward (3 μL).
+
+4. Licking the incorrect lickport triggered a timeout (2-6 s). 
+
+5. Licking early during the trial was punished by a loud \'alarm\'
+sound, followed by a brief timeout (1-1.2 s). Continued licking
+triggered additional timeouts; these trials were excluded from the
+analyses (“lick early” trials). 
+
+This task could also be modified several ways: 1) removing the delay
+period (allows faster training); 2) using a row of whiskers instead of
+just a single one; 3) using a motorized lickport that is presented
+when the response period begins instead of a go tone; 4) using a
+sucrose-sweetened reward instead of plain water (sometimes interleaved
+sesssion-wise). 
+
+
+#### Variation: Lick/No-lick Location Discrimination task
+
+Used in training, to train mice to use a single whisker (typically C2)
+to locate a vertical pole for a water reward. Similar to the
+left/right task, with the following changes: 
+
+1. Only one lick spout centered on midline.
+2. The no-lick position was a single anterior pole location. The lick
+   position is one, or multiple, relatively posterior pole locations. 
+3. Movement of the pole took 0.5 s, after which the animal was
+   given 2.5 s to search for the object with its whisker and indicate
+   object location by licking or withholding licking.
+4. The mouse is given a grace period (0.5–1.5 s) from onset of pole
+   movement where licking does not signal the response outcome. 
+5. Hits triggered opening of a water valve to deliver approximately
+   8uL of water. 
+6. Two seconds after the answer lick, the pole retracted and the
+   intertrial period begins (~2s). 
+7. On false alarm trials the mouse is given a timeout, typically
+   2–5s, which retriggered on any additional licks during the
+   timeout. If no lick occurred during the response window, the trial
+   was scored as a miss (lick trial) or a correct rejection (no-lick
+   trial).
+
+
+Per session metadata:
+* Inter-trial period duration
+* reward volume (~4uL)
+* reward type (water/sucrose-water, interleaved daily)
+
+Per trial metadata:
+* Pole position
+* ...
+
+
+
+### Stimulus
+
+Should check individual MAP references to see variations in pole
+positions used (see Guo et al, sometimes multiple pole positions used
+all corresponding to one 'lick' condition, in training etc.)
+
+* Modality: Somatosensory/Auditory
+* Stimulus type: Metal pole
+* Variable parameters: Pole position (A/P)
+* 'Go' (response) tone (pure tone, 3.4 kHz, 0.1 s duration)
+
+From Nuo: 'The stimulus is a pole (0.9 mm in diameter), presented at
+one of two possible positions. The two pole positions were 4.29 mm
+apart along the anterior-posterior axis (40 deg of whisking angle) and
+were constant across sessions. The posterior pole position was 5 mm
+from the whisker pad.'
+
+From Guo et al: 'We have also observed that the distance of the pole
+from the whisker pad has a large impact on performance. The whisker is
+linearly tapered and its bending stiffness decreases gradually with
+distance from the whisker pad over five orders of magnitude.' 
+
+
+
+### Registration of spatial coordinates
+
+* Nathan and Alan (Vidriotech) told us that for the visualizations
+  that Dave Liu showed at his poster they are using an older version
+  of the mouse CCF, not sure why? This is for the Neuropixels data.
+
+
+
+### Genotype/strain metadata
+
+From Li et al (2015), 52 mice in total:
+
+1. VGAT-ChR2- EYFP mice (Jackson laboratory, JAX Stock #014548)
+
+2. PV-ires-Cre45 crossed to Rosa26-LSL-ReaChR, red-shifted
+channelrhodopsin reporter mice (JAX 28846), were used for
+photoinhibition experiments.
+
+3. Sim1_KJ18-Cre mice (MMRRC 031742), Rbp4-Cre mice (MMRRC 031125),
+   and Tlx_PL56-Cre mice (MMRRC 036547) were used for
+   electrophysiology experiments.
+
+4. C57Bl/6Crl mice were used for imaging experiments.
+
+5. Sim1_KJ18- Cre crossed to Ai32 (Rosa26-ChR2 reporter mice, JAX
+   Stock #012569) mice were used for photoactivation behavioural
+   experiments, and one of these mice was also used for
+   electrophysiology. 
+
+6. Tlx_PL56-Cre crossed to Ai32 mice were used for photoactivation
+   behaviour experiments and two of these mice were also used for
+   electrophysiology.
+
+7. Sim1_KJ18-Cre, Tlx_PL56- Cre, C57B1/6Crl, Sim1_KJ18-Cre 3
+   Ai32, and Tlx_PL56-Cre 3 Ai32 mice were used for anatomy
+   experiments. 
+
+And viral injections:
+
+1. 'To characterize BAC Cre mice we injected eGFP
+(AAV2/1.CAG.EGFP, http://www.addgene.com, plasmid 28014) into one
+hemisphere and Cre-dependent tdTomato (AAV2/1.CAG.FLEX.tdTomato.WPRE,
+UPenn Viral Core, AV-1-ALL864) into ALM on the other hemisphere.'
+
+2. 'To optogenetically tag ALM intratelencephalic and pyramidal tract
+   neurons during recording, we first infected ALM neurons with
+   ChR2. Cre-dependent ChR2 virus (AAV2/5.hSyn1.FLEX.hChR2.tdTomato,
+   http://www.addgene.com, plasmid 41015) was injected into three
+   Rbp4-Cre mice (targeting both layer5 intratelencephalic and
+   pyramidal tract neurons), four Tlx_PL56-Cre mice (layer 5 intrate-
+   lencephalic neuron), and nine Sim1_KJ18-Cre mice (pyramidal tract
+   neurons). One-hundred-nanolitre volumes were injected 500 and 800
+   mm deep. We also used two Tlx_PL56-Cre cross Ai32 transgenic mice
+   for antidromic tagging of intratelencephalic neurons.'
+
+3. 'AAV2/1-syn-GCaMP6s-WPRE virus (UPenn Viral Core, AV-1-PV2824) was
+   diluted two- to sixfold in HEPES buffered saline. Injections were
+   made at three to five locations centred around ALM (separated by
+   ,400 mm) and at three depths (210/370/530 mm) for each location
+   (,5–6 nl per depth)' 
+
+
+## Questions/Next steps
+
+* Is this all the mouse strains/genetic tools they use? Check most
+  recent papers/ask Nuo. 
+* Nuo has given us an FSM implementation of the left/right task (see PDF).
+
+
+
+## References
+
+1. Guo, Z. V. et al. Procedures for behavioral experiments in
+head-fixed mice. PloS One 9, e88678 (2014).
+
+2. Li, N., Chen, T. W., Guo, Z. V., Gerfen, C. R. & Svoboda, K. A
+motor cortex circuit for motor planning and movement. Nature 519,
+51-56 (2015).
+
+
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+