projects-start/ideas.md

---
tags: open, questions, query, projects, lab, collaboration    
dateOriginal: 2016-05-18 14:18:20  
date: 2016-10-06 10:04:44  
title: projects-start  
---

Welcome to the ackmanlab projects-start page! The following is a some queries for the lab and local community. The items are not necessarily listed in a particular order/priority.

## Experiments

Many of these require designing and performing new experiments...

### Neural activity manipulation

* Can we manipulate sensory input patterns with DREADDs and see corresponding changes in cortical wave activity (transgenic mouse retinal-cre-DREADDs experiment)?
* Can we manipulate intra-cortical input patterns with DREADDs and see corresponding changes in cortical wave activity (intra cerebral AAV-DREADDs injection experiment)?
* Can we manipulate intra-cortical input patterns with red-shifted optogenetics and see corresponding changes in cortical wave activity?
* Is cortical wave activity the same in pan neuronal gcamp6 vs upper layer gcamp6 mice? What about deeper layers? At all developmental ages? Implications for causative role of spontaneous cortical waves with inter-areal synaptic development?


### Sensory stimulation

* How does early brain activity predict behavior? Is there a functionally asymmetric activity pattern that predicts lateralized behavior (paw preference)?
* What are the non-mirror symmetric activity patterns between the hemispheres for (trunk limb 'spirals and circles' in the fMOI movies)?
    * Are these patterns related to inter-hemispheric feed-forward inhibition? Different flexor/extensor or motor neuron pools? Limb abduction or adduction movement sequences? Is it different in mice with bad balance or locomotion? What about swimming?
* Does abduction (away from body core) and adduction (towards body core) of the forelimbs/paws map to distinct fMOI activation patterns?
* Can we map moving bar stimuli of speeds/frequencies to fMOI in visual cortex in 2-3 wk old mice?
* Can we map auditory frequencies/amplitude to fMOI in auditory cortex in 2-3 wk old mice?
* Can we present desirable or aversive complex/simple odorants/tastes during development and see fMOI activation patterns? Can we do this in mice at 2+ wks of age to localize brain activitions associated with sibling/rival game dynamics or a model for empathy testing?

### Genes/mouse models

* Are inter-hemispheric activity patterns and associations different in acallosal mice? What does this tell us about the contribution of inter-hemipheric vs sub-cortical inputs for inter-areal activity correlations?
* Is global cortical activity patterns clearly altered in an autism or schizophrenic mouse model?
* Are immediate early genes (IEG) activated during/between cortical waves in developing mice? If so, which ones? Is there differential activation during cortical-sensory input deprivation during development (retinal, cochlear, limb ablations)



### Environment

* What does administration of a serotonin-reuptake inhibitor do anything to fMOI cortical wave activity?
* How different is global cortical activity during light isoflurane anesthesia? During ketamine anesthesia? During hypothermia? During tamoxifen injections?
* Does chronic environmental exposure to a heavy metal during fetal/postnatal development in mouse alter global or local cortical activity patterns?
* How much of the cortex is activated during an ictal events/seizure in an fMOI movies? How essential is the callosum (vs anterior or hippocampal comissure) for cross-hemisphere events or severity?


### Cortical waves

* Are cortical wave properties (velocity, wavefront pattern) during development related to topographic discrimination/receptor density (retina/V1 vs whiskers/barrel cortex) mapping of the sensory periphery?
* What is the relation between developmental calcium domains functional units/cortical modules in isocortex?
* Do the spatiotemporal dynamics of cortical-calcium waves map to cerebral cortical areas across brain development? How early? Is is simultaneous with the emergence of some anatomical/molecular marker for cortical areal formation?
* Evolutionary ontogeny of retinal waves in early vertebrates
    * Make gcamp chicks? in ovo trans-shell imaging? 
    * Is it possible to make transgenic (gcamp6) turtles (make earliest amniote vertebrate model for retinal waves)?
    * Could the longer gestation time (40 - 60 d.) be used as an advantage over mice to study the effect of developmental time (no. of wave iterations) on neural activity dependent structural pattern formation?

### Other

* Can we image the cerebellum? Is it's activity coordinated with that of isocortex? *(cerebellum is still developing postnatally and the deep cerebellar connections still are still functionally integrating with thalamus). If the cerebellum functions as an error detector, what does its coordination (or lack of) with cortex during development tell us about cortically driven behavioral output (maybe its OFF early than ON late like after eye opening?)*
* Why does a developmentally regulated correlation between PPC & RSA and limb movement activity exist? Transient synaptic formation/strengthening followed or silencing while waiting for behaviorally relevant sensation/decision making to occur? What brain areas do they 'talk to' during development?
* Are cortical activation patterns in RSA/PPC associated with hippocampal synchronous oscillations ('giant depolarizing potentials') during development?
* Does the classic monocular deprivation/ocular dominance shifting experiments in P20-P28 mice do anything to global inter- or intra-cerebral fMOI activity patterns?
* Is there a 'phantom limb' activation pattern in mice after limb ablation? Is there increased co-activation with regions that have been implicated in pain/self/body core (cingulate,retrosplenial (RSA) cortex)? Is it different/better at earlier ages? Can it be reversed?


### Ephys, Behavior

* Are fMOI cortical wave patterns strongly associated with different EEG/LFP frequencies (delta, alpha, theta, gamma) during different behavioral states in 2-3 wk old mice?
* Can we perform cell attached blind patch clamp recordings simultaneously with fMOI? *Implications for activity of individual neurons during cortical waves, can get cell 'golgi' like morphology with biocytin fills*
* Can we see paw preferences in 2-3 week old mice?
* Can we measure optokinetic response behavior in 2-3 week old mice? *Measure of absolute visual function. Prusky work suggest this should be possible*
* Can we measure water maze/visual acuity behavior tracking on 2-3 week old mice? *Measure of cortically mediated visual function, should be possible at 4-5 wk mice but how about just after eye opening (how quickly can they be trained?)*
* Can we detect evidence for any kind of reverbatory wave 'memory' trace from a recently experienced event (a multimodal aversive or rewarding stimulus (air puff, drop, shaking, swimming)? a **moving** looming object in space (vision +/- sound) in a particular direction?) in developing mice?
* Can we perform coupled imaging of two animals with realtime activity or behavioral detection and sensory feedback on the rig? Can this be used to social/behavorial development (can we make friendly/outgoing vs aggressive mice? Ones that prefer or are aversive to tactile vs visual vs auditory vs olfactory cues)? Does this cause changes in the strength of synaptic connections and later behavioral preferences? Can these changes then be reversed or is there a 'critical period'?
* Video monitoring and descriptive quantification of behavior during development for limbs, eyes, whiskers, jaw, respiration, heart rate, temperature
    * Implement workflow for measuring multiple time variant (milliseconds <–> minutes) physiological signals simultaneously in a freely behaving mammal while recording whole cerebrum neural wave patterns


### Cellular development

* Do retinal waves influence glial development? Do microglia mediate the effects of retinal waves on visual synaptic connectivity?
* Do retinal waves influence interneuron migration/maturation during early postnatal development?
* Are retinal waves utilized for callosal projection targeting of axons?
* Are there any evidence for interareal functional connections that are active early in development during any or all behavioral states then become silent? Implications for selectionist vs constructionist learning paradigms across cell assemblies?
* Immediate early gene (IEG) expression in cortical areas with disrupted activity patterns (isoflurane experiments, pharmacogenetic/DREADDs, peripheral ablation of retina/cochlea/whisker pad)


## Analyses

Many of these can be answered by implementing new analyses on existing data...

### Waves

* Do retinal waves regulate motor activity (are developing mice more likely to 'wake up' at the beginning or ending of a retinal wave)?  
	* Could this be important for wiring together and preparing circuitry necessary for innate visual behavior (e.g. linking visual responses such as a moving shadow from an owl in the sky to attention/motor action)?
* Which brain areas are active during retinal waves with PSTH analysis? Wave form average?
* Do retinal waves drive higher order cortical areas (like the M2/FEF or RSA)?
* Is there an area in M2/cingulate like the FEF/FOF (frontal eye/orienting field) that is active around retinal waves at any particular age? Does this argue for a strength of fMOI in analysing global inter- vs intra- cerebral functional activity patterns?
* Does the similarity (directionality, velocity, wavefront size, failure rate) of retinal wave activation between the superior colliculus and V1 increase during development? Does the failure rate of wave front propagation decrease?



### Function

* Can clustering/pca break joint cortical activity/body motion movies into distinct (and possibly mixed/overlapping) behavioral states? *Test distance measures/clustering techniques (Kmeans, Mahalanobis, PCA, etc) space-time data matrices containing some brain activity signals and body signals (limb motion, face/whisker/jaw motion, respiratory rate and see if some general physiological states can be segmented (e.g. quiet sleep (no motion), active sleep (motion), wakefulness)*
* Do global activity patterns then cluster into distinct components based on behavioral state (e.g. quiet sleep, active sleep, wakefulness)?
* What are global cortical wave patterns for-- do they cluster into different motifs during different behavioral states or sensory activations? Can they represent functionally associated, **inter-areal cell assemblies**?
* In what fraction of our videos can we see whisker/mystacial pad movements?
* Can we see eye movements (e.g. eyelid vibrations) in our existing videos?
* Can we identify jaw movements in our existing videos?
* Which regions are active around limb movements with PSTH analysis? 'Spike' triggered wave form average?
* Can we map cortical areas based on tactile stimulations (limbs/faces) present in existing wholebrain data videos? #function #codework


### Connectivity

* What fraction of other Allen connectivity atlas isocortex regions (besides VISp) have particular long distance intra-cerebral connection patterns?
* Which brain regions are 'driver nodes' (high eig centrality, low betweeness centrality)? Does it change during development?
* Are cortical hubs from fMOI association matrices the same as those predicted by the Allen connectivity atlas?
* Are cortical activity maps from fMOI similar to those of structural connection patterns from the Allen Brain atlas?
* Does a finer grain/higher density ROI analysis of the cortical association matrix give a similar number and membership of network modules? 



## Hardware/software

* [x] acquire video with microcontroller/[raspberry pi](https://github.com/ackmanlab/RaspberryPi-Setup)
* acquire pco edge 5.5 sCMOS video with labview
* [x] acquire pco edge 5.5 sCMOS video directly into openCV @brmullen 2017
* [ ] custom pulse oximeter for young mice
    * transmissive pulse oximetry, pass two wavelengths through body part to photodetector, measure absorbances, ratio of red to infrared light absorbtion at measuring site to infer O2 saturation levels. Relies on hemoglobin saturation. [O2 saturation meter with red and green filters dating to 1935](https://en.wikipedia.org/wiki/Pulse_oximetry)
    * reflective pulse oximetry
* [ ] **tissue biopsy device** (glass pipette and suction) and motor controller for localized tissue resection (e.g. RNAseq) during functional imaging
* visual behavior
    * prusky visual water maze
    * VR software spatial navigation
    * eye movement tracking
* auditory behavior
    * get microphone with good ultrasonic frequency detection, hook up to amplifier and acquire/trigger through microcontroller/NI
    * ultrasonic vocalization tracking with labview-- animal colony
    * speakers in with nidaq for auditory stimulation
* sensory/tactile behavior
    * laser microstimulation tactile mapping, dmd?
    * multiple channel solenoid airpuff delivery around body
    * mouse sitting on capacitive touch screen for positional tracking
* olfactory/gustatory behavior
    * presentation of desirable or aversive complex/simple odorants tastes
* motor movements
    * eye movement tracking
    * whisker movement tracking
    * stereovideo --> disparity information by frame --> 3D motion vector 
* system behavior
    * limb reaching detection
        * [x] computer vision for left vs right paw @brmullen @
        * rfid chip glued to limbs and microcontroller based scanner (good also for confirming cv location)
        * [ ] IR or fluorescent paint on limbs
        * [x] reflective paint on limbs
    * morris watermaze and video tracking (without functional cortical imaging)
    * piezo controller for updown rapid movement for waterbath swimming (with functional cortical imaging)
* imaging/optics
    * [x] functional widefield meso/macro imaging rig with large FOV
    * [x] Illumination optimization on widefield meso/macro imaging rig
    * [x] Test functional imaging with one or multiple raspbery pi type cameras *Rationale: Can functional meso imaging be done with cheaper hardware? Implications for scalability? Can **multiple** consumer 8 bit cameras be used simultaneously and post processed in opencv to simulate/achieve higher dynamic range? Does this help also with signal resolution and denoising or deconvolution?*
    * [ ] Perform more inexpensive cmos camera testing-- multiple lower dynamic range cameras together (and for stereovision)?
    * [ ] Interleaved 2 color channel imaging *Rationale: help isolate signal artifacts (blood vessel/motion) not directly stemming from cortical activity?* 
    * [ ] lab widefield **microscope** with thorlab components for general histology
    * structured illumination for optical stimulation control
    * lab structured illumination confocal imaging
    * SLM microscope (R. Yuste and Darcy Peterka work)
    * lab 2P microscope with thorlab components
* data IO
    * 10GigE lab intranet
    * local data server/processor


## software/informatics

* [pyWholeBrain](https://github.com/ackmanlab/pyWholeBrain) #codework #function
    * [x] dFoverF functionality
    * [x] opencv video playback
    * [x] timecolormap proj in opencv/python #codework
    * [x] and many others...
    * [x] python ec2 SVD/PCA
    * [x] python ICA
* **Python figure/image drop app**–
    * [x] implement AWS Lambda image processing api functionality
        * [x] with graphicsmagick
    * [x] python script for markdown notebook/lab db/AWS S3 store #informatics #devices #codework
    * [] javascript/html (os agnostic) node app for auto image upload
* Animal database web app
    * translate old movie recording db to new animal db
    * add functionality to google sheet --> add webhooks?
        * python qt/tkinter gui/ html5 webform for experimental information input (from acquistion PC or webform) to populate animal database
    * [x] Delimited text file db (tsv, json) for serving through github or AWS S3
    * AWS DynamoDB or SQL
        * [x] webhooks integration for github, AWS, Slack notifications, mobile phone webhooks (pythonista, IFFT/Drafts web app for android/iOS) #informatics #mice #codework
    * animal database QR codes for cage cards
    * [x] wholebrain experimental database, data in s3, sql web database in ec2 instance #codework #informatics
* [x] realtime dF/F normalization/scaling in opencv #codework #devices
* allen brain atlas informatics--
    * [x] implement python interaction with ABI
    * [x] fetch ABI mouse connectivity data arrays
    * [x] isolate and parse isocortex projections in ABI connectivity data arrays
    * [x] compute structured connection similarity between pairs of brain regions
    * [ ] compute structured (ABI data) to functional (our brain activity data) connection similarities within brain regions
    * [ ] ABI proj xyz proj model--> fit widefield signal decay functions to top down view to infer wholeBrain signals #codework #connectivity
    * [ ] ABI proj pattern wave correlation #codework #waves #function
* [x] amazon ec2 virtual machine #informatics
* Spark array concat -- python ec2 svd/pca #informatics #codework #function
* Machine learning detection of wave pattern classes #codework #function #waves #informatics
* [x] Machine learning detection of brain ROIs #codework #function #waves #informatics
* Wavelet denoising #function #codework
* Exploratory data analysis/informatics–
    * AWS video upload mp4 movie conversion and time color map projection trigger --> populate internal html5 page
    * R/html5 graph exploration #informatics #codework
    * R/html5 gui sliders for quantified metrics #informatics #codework
* Visual stimuli in psych or python toolbox for visual acuity testing #devices #function #codework
* [ ] developing mouse atlas based on parcellation positions in functional maps
* asymmetric gene expresion in embryo to implement hemispheric manipulation strategy
* Does the velocity of manually observed cortical waves match that of computed with that with optical flow/computer vision techniques? *Plot manually observed vs cv detected retinal wavefront speeds from primary visual cortex*
* alexa append CV, log
* explore UC3 Dash tool as data archive, public movie sharing tool