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fall 2017 update

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--- ---
tags: open, questions, query, projects, lab, collaboration tags: open, questions, query, projects, lab, collaboration
date original: 2016-05-18 14:18:20 dateOriginal: 2016-05-18 14:18:20
date: 2016-10-06 10:04:44 date: 2016-10-06 10:04:44
title: projects-start title: projects-start
--- ---
@@ -48,7 +48,12 @@ Many of these require designing and performing new experiments...
### Cortical waves ### 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? * 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?
* Is it possible to make transgenic (gcamp6) turtles (make earliest amniote vertebrate model for retinal waves)? * 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 ### Other
@@ -69,6 +74,7 @@ Many of these require designing and performing new experiments...
* 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 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'? * 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 * 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 ### Cellular development
@@ -121,23 +127,24 @@ Many of these can be answered by implementing new analyses on existing data...
* [x] acquire video with microcontroller/[raspberry pi](https://github.com/ackmanlab/RaspberryPi-Setup) * [x] acquire video with microcontroller/[raspberry pi](https://github.com/ackmanlab/RaspberryPi-Setup)
* acquire pco edge 5.5 sCMOS video with labview * acquire pco edge 5.5 sCMOS video with labview
* acquire pco edge 5.5 sCMOS video directly into openCV * [x] acquire pco edge 5.5 sCMOS video directly into openCV @brmullen 2017
* custom pulse oximeter for young mice * [ ] 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) * 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 * reflective pulse oximetry
* **tissue biopsy device** (glass pipette and suction) and motor controller for localized tissue resection (e.g. RNAseq) during functional imaging * [ ] **tissue biopsy device** (glass pipette and suction) and motor controller for localized tissue resection (e.g. RNAseq) during functional imaging
* visual * visual behavior
* prusky visual water maze * prusky visual water maze
* VR software spatial navigation * VR software spatial navigation
* eye movement tracking * eye movement tracking
* auditory * 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 * ultrasonic vocalization tracking with labview-- animal colony
* speakers in with nidaq for auditory stimulation * speakers in with nidaq for auditory stimulation
* sensory/tactile * sensory/tactile behavior
* laser microstimulation tactile mapping, dmd? * laser microstimulation tactile mapping, dmd?
* multiple channel solenoid airpuff delivery around body * multiple channel solenoid airpuff delivery around body
* mouse sitting on capacitive touch screen for positional tracking * mouse sitting on capacitive touch screen for positional tracking
* olfactory/gustatory * olfactory/gustatory behavior
* presentation of desirable or aversive complex/simple odorants tastes * presentation of desirable or aversive complex/simple odorants tastes
* motor movements * motor movements
* eye movement tracking * eye movement tracking
@@ -145,17 +152,19 @@ Many of these can be answered by implementing new analyses on existing data...
* stereovideo --> disparity information by frame --> 3D motion vector * stereovideo --> disparity information by frame --> 3D motion vector
* system behavior * system behavior
* limb reaching detection * limb reaching detection
* computer vision for left vs right paw * [x] computer vision for left vs right paw @brmullen @
* rfid chip glued to limbs and microcontroller based scanner (good also for confirming cv location) * rfid chip glued to limbs and microcontroller based scanner (good also for confirming cv location)
* IR or fluorescent paint on limbs * [ ] IR or fluorescent paint on limbs
* [x] reflective paint on limbs
* morris watermaze and video tracking (without functional cortical imaging) * morris watermaze and video tracking (without functional cortical imaging)
* piezo controller for updown rapid movement for waterbath swimming (with functional cortical imaging) * piezo controller for updown rapid movement for waterbath swimming (with functional cortical imaging)
* imaging/optics * imaging/optics
* [x] functional widefield meso/macro imaging rig with large FOV * [x] functional widefield meso/macro imaging rig with large FOV
* [ ] Illumination optimization on widefield meso/macro imaging rig * [x] Illumination optimization on widefield meso/macro imaging rig
* [ ] 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?* * [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?*
* interleaved 2 color channel imaging *Rationale: help isolate signal artifacts (blood vessel/motion) not directly stemming from cortical activity?* * [ ] Perform more inexpensive cmos camera testing-- multiple lower dynamic range cameras together (and for stereovision)?
* lab widefield **microscope** with thorlab components for general histology * [ ] 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 * structured illumination for optical stimulation control
* lab structured illumination confocal imaging * lab structured illumination confocal imaging
* SLM microscope (R. Yuste and Darcy Peterka work) * SLM microscope (R. Yuste and Darcy Peterka work)
@@ -170,21 +179,27 @@ Many of these can be answered by implementing new analyses on existing data...
* [pyWholeBrain](https://github.com/ackmanlab/pyWholeBrain) #codework #function * [pyWholeBrain](https://github.com/ackmanlab/pyWholeBrain) #codework #function
* [x] dFoverF functionality * [x] dFoverF functionality
* [x] opencv video playback * [x] opencv video playback
* [ ] timecolormap proj in opencv/python #codework * [x] timecolormap proj in opencv/python #codework
* [ ] numerous other tasks on project repo page * [x] and many others...
* [x] python ec2 SVD/PCA
* [x] python ICA
* **Python figure/image drop app**– * **Python figure/image drop app**–
* for automating handheld image to markdown notebook/lab db/AWS S3 store #informatics #devices #codework * [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 * Animal database web app
* translate old movie recording db to new animal db
* add functionality to google sheet --> add webhooks? * 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 * python qt/tkinter gui/ html5 webform for experimental information input (from acquistion PC or webform) to populate animal database
* Delimited text file db (tsv, json) for serving through github or AWS S3 * [x] Delimited text file db (tsv, json) for serving through github or AWS S3
* AWS DynamoDB or SQL * AWS DynamoDB or SQL
* webhooks integration for github, AWS, Slack notifications, mobile phone webhooks (pythonista, IFFT/Drafts web app for android/iOS) #informatics #mice #codework * [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 * animal database QR codes for cage cards
* wholebrain experimental database, data in s3, sql web database in ec2 instance #codework #informatics * [x] wholebrain experimental database, data in s3, sql web database in ec2 instance #codework #informatics
* realtime dF/F normalization/scaling in opencv #codework #devices * [x] realtime dF/F normalization/scaling in opencv #codework #devices
* allen brain atlas informatics-- * allen brain atlas informatics--
* [x] implement python interaction witwh ABI * [x] implement python interaction with ABI
* [x] fetch ABI mouse connectivity data arrays * [x] fetch ABI mouse connectivity data arrays
* [x] isolate and parse isocortex projections in ABI connectivity data arrays * [x] isolate and parse isocortex projections in ABI connectivity data arrays
* [x] compute structured connection similarity between pairs of brain regions * [x] compute structured connection similarity between pairs of brain regions
@@ -194,13 +209,16 @@ Many of these can be answered by implementing new analyses on existing data...
* [x] amazon ec2 virtual machine #informatics * [x] amazon ec2 virtual machine #informatics
* Spark array concat -- python ec2 svd/pca #informatics #codework #function * Spark array concat -- python ec2 svd/pca #informatics #codework #function
* Machine learning detection of wave pattern classes #codework #function #waves #informatics * 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 * Wavelet denoising #function #codework
* Exploratory data analysis/informatics– * Exploratory data analysis/informatics–
* AWS video upload mp4 movie conversion and time color map projection trigger --> populate internal html5 page * AWS video upload mp4 movie conversion and time color map projection trigger --> populate internal html5 page
* R/html5 graph exploration #informatics #codework * R/html5 graph exploration #informatics #codework
* R/html5 gui sliders for quantified metrics #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 * Visual stimuli in psych or python toolbox for visual acuity testing #devices #function #codework
* developing mouse atlas based on parcellation positions in functional maps * [ ] developing mouse atlas based on parcellation positions in functional maps
* asymmetric gene expresion in embryo to implement hemispheric manipulation strategy * 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* * 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