Sep 2 Mon Labor day @ Flatiron

Learning React. why? it ties model view controller framework. Imagine what I can do if I can expose the controls through the web. My work will be completely visible and usable by the users through the web interface. react is the fastest way to get the scientific tools to the users. JSX + react allows easy integration with the python backend. this is why I must learn react. it’s tied to Jeremy’s new visualization effort (reactopya) and it’s a very scalable way to design scientific visualization. Combined with kb-snapshot (model), spikeforest (controller), reactopya (view) it allows full integration of the flatiron pipeline. Now it’s time to build a strong well integrated system.

The ultimate goal is to implement all neural processing routines on the web and work with Jeremy to realize this dream. Break the boundary and make the data available anywhere everywhere. Let the web technology transform the way science is conducted. I bet CZI has similar vision.

Built-in Javascript functions

  • setInterval(fh, milliseconds)
  • new Date().toLocaleTimeString()

Built-in react functions

  • ReactDOM.render(element, document.getElementById(‘root’))
  • const element = (); #declare
  • React.Component doc

Canada health research government grants and contracts inurl:gc.ca

Canada trade commissioner services
Canada start business (startup)
Can export innovation (going global funding)
Application
Canada innovation funding support
SBIR like programs in Canada
CSA funding opportunities and grants

Partners
Reza Khanbabaie google scholar

Life sciences research bodies
Genome Canada
http://www.genomecanada.ca
Offers primary funding and an information resource for genomics and proteomics in Canada.

Health Canada
http://www.hc-sc.gc.ca
Provides national leadership in enhancing healthy living, responding to the changing nature of health issues, and promoting disease prevention.

International Development Research Centre (IDRC)
http://www.idrc.ca
Supports research in developing countries to promote growth and development.

National Research Council Canada (NRC)
http://www.nrc-cnrc.gc.ca
NRC institutes in the field of life sciences specialize in the development of biopharmaceutical and medical devices and foster international research linkages.

Funding Programs
Canadian Institutes of Health Research (CIHR)
http://www.cihr-irsc.gc.ca
Support over 14,000 researchers and trainees in the creation of new health research knowledge and its translation into improved health for Canadians.

Canada Foundation for Innovation (CFI)
http://www.innovation.ca
Supports more than 7,000 projects across Canada that lead to breakthroughs in areas such as health.

Going Global Innovation (GGI)
http://www.tradecommissioner.gc.ca/eng/science/going_global.jsp
Promotes Canada’s innovation efforts by supporting Canadian researchers to solidify partnerships with international key players for science-based research and development projects that have commercial potential.

Natural Sciences and Engineering Research Council of Canada (NSERC)
http://www.nserc-crsng.gc.ca
Supports some 30,000 post-secondary students and post-doctoral fellows and 12,000 professors every year.

Social Sciences and Humanities Research Council of Canada (SSHRC)
http://www.sshrc-crsh.gc.ca
Promotes and supports post-secondary based research and training in the humanities and social sciences to enhance our understanding of modern social, cultural, technological, environmental, economic, and wellness issues.

Explore the Possibilities
A comprehensive list of programs and information on education in Canada
http://www.educationau-incanada.ca
Partnership opportunities and information on innovation projects
http://www.tradecommissioner.gc.ca/eng/science/home.jsp
Profiles on cutting-edge research at institutions across Canada
http://www.InnovationCanada.ca
http://www.science.gc.ca
International scholarships and fellowships
http://www.scholarships.gc.ca
http://www.nserc-crsng.gc.ca
Association of Universities and Colleges of Canada
http://www.aucc.ca
Association of Community Colleges of Canada
http://www.accc.ca

chalk talk

NSEEC industry.

Bickle foundation. high risk high reward.

NSERC grant. Cross-modal measurement of in-vivo spiking activities from the known cell-types (Neural recoding + analysis)

Aim1. Develop cross-modal electrophysiology recording and stimulation capability combined with optical recording and stimulation at the brain-wide, cellular resolution.

polymer microelectrodes, microLED, transparent glass electrodes, multifunctional probes

Aim2. Generate electro-optical groundtruth recordings by tracking the spiking activities of known cell types over multiple days, and use them to validate existing spike sorting and Ca image analysis algorithms.

Aim3. Develop online analysis software to analyze the electrical and optical recordings in real-time.

Implement algorithms using real-time OS, FPGA, and


NSERC grant. Develop AI-based predicitve neuroinformatics platform for distributed computing environment

Aim 1. Develop web-based platform to benchmark existing neural decoding algorithms using publicly available neural recordings paired with behavioral or sensory recordings.

Based on SpikeForest pipeline in collaboration with Flatiron Institute. Combines calcium imaging analysis, spike sorting analysis, behavioral analysis. Uses IBL and Allen brainobservatory dataset

Aim 2. Develop algorithms to predict voluntary decisions animals make during spatial navigations using existing datasets.

T-maze. W-maze. accuracy and predictive time window evaluation. LFP and spiking information. phase

CIHR grant. Neurodynamics during social functions in normal and autistic brains

I am interested in studying synchronized neurodynamics in a pair of socially interacting animals under naturalistic conditions.
In particular, I want to understand how social behaviours are perceived and generated in distributed brain areas including the auditory and motor cortex, amygdala, and hippocampus.
Mice vocalize at ultrasonic frequencies and I want to investigate how various communication signals play a role in synchronizing neural states in healthy individuals as well as a mouse autism model [6].
The understanding gained from this research may reveal novel biological markers for autism spectrum disorder (ASD) based on key factors distinguishing autistic and healthy brains in perceiving and expressing vocal communication.
In addition, long-term neural recordings in multiple brain regions could reveal a circuit-level action of pharmacological agents such as R-Baclofen, which has been recently developed and clinically evaluated to treat the symptoms of ASD.
One of the hallmarks of ASD is an enhanced ability to recognize fine perceptual details while missing out on a larger context.
By using ultrasonic vocalization as a behavioural assay, I want to measure how various stages of sensory (auditory) information processing are affected by ASD and understand the action of R-Baclofen in inducing neuroplasticity over an extended period.
Recently, functional brain stimulation is beginning to replace pharmacological treatments for various neurological conditions including Parkinson’s disease, epilepsy, and depression to overcome drug resistance and unintended side effects.
Based on understanding the circuit-level mechanism of R-Baclofen, I want to explore targeted neurostimulation to achieve similar effects in the animal models of ASD.
My initial approach would be to apply a machine-learning driven bidirectional neural interface to detect and interfere with pathological neurodynamics as well as to induce neuroplasticity that affects the resting brain state.

Multimodal brain activity measurement papers

Multimodal Characterization of Neural Networks Using Highly Transparent Electrode Arrays

Euisik yoon group Mendrela thesis

Optogenetic-fMRI arousal networks

Ottawa small animal MRI: see Georg Northoff
Syringe-injectable mesh electrodes (Lieber group)

EEG and fMRI (thesis) sleep deprevation 2018
Simultaneous gcamp+fMRI (2017)

Diversity of sharp-wave–ripple LFP signatures reveals differentiated brain-wide dynamical events (2015)

# Theory
Variational inference (David Blei). Edwardlib.org

# Neuroscience research funding
https://can-acn.org/neuroscience-research-funding-opportunities

Funding applications

# Canadian funding
researchnet.ca
NSERC discovery grant: Aug1 notification of intent, Nov 1 application
NSERC CREATE Grant: Collaborative research and trainig experience training. $1.65M for 6 years
Compute Canada: Nov 8
NSERC discovery grant: Aug1 notification of intent, Nov 1 application
NSERC CREATE Grant: Collaborative research and trainig experience training. $1.65M for 6 years
Albertainnovates.ca:
DND/NSERC grant:
NSERC CREATE
NSERC research tools and instruments: 150K (OCT 25)
NSERC training video
CIHR grants (researchnet)
CFI grant
New frontiers in research fund (international, fall 2019). (Exploration Aug 7, Sep 4. $125K/year, 2 years)
New Frontiers Transformation (2019 competition)

# Private funding
Simons foundation: Winter 2020 pilot. $300K for two years. Sep 13. New to autism.
Simons Bridge to independence. $500K for 3 years. LOI due Aug 8 2020.

CZI: https://chanzuckerberg.com/rfa/essential-open-source-software-for-science/ (closed on Aug 1)
250K for 1 year
HHMI
KECK foundation:

# US Grants
Participation by Canadian Researchers in the NIH BRAIN Initiative
Team Grant : Next Generation Networks for Neuroscience (NeuroNex) from CIHR and NSF (2019 Dec 13)

# EU grants
https://www.neuron-eranet.eu/en/196.php
https://www.hfsp.org/funding/hfsp-funding/research-grants (Mar18)

# Neuropixels resources
Neuropixels from cortex lab
https://github.com/cortex-lab/neuropixels/wiki/Equipment_List
https://www.neuropixels.org/

International brain lab
https://github.com/int-brain-lab/iblrig

# Chronic implementation

Neuropixels chronic implantation
https://www.biorxiv.org/content/10.1101/406074v1.full

# Chronic surgery
MRI compatible CMOS
https://ieeexplore.ieee.org/abstract/document/8116684
Tim Hanson’s neural sewing machine
https://www.biorxiv.org/content/10.1101/578542v1
https://www.biorxiv.org/content/10.1101/578542v1
Power of small animal fMRI

https://www.frontiersin.org/articles/10.3389/fphar.2015.00231/full
#Reverse engineering visual intelligence (Jim DiCarlo)
https://www.youtube.com/watch?v=3djQSX1FJ9I
Using goal-driven deep learning models to understand sensory cortex

Figure 1

# Intel Telluride Neuromorphic cognition engineering workshop
3-week hand-on work
https://sites.google.com/view/telluride2019/about-workshop?authuser=0

# MRI compatibility of pacemaker

ok according to Harvard Men’s health watch
MRI safe metals: copper, cobalt-chromium, Titanium, stainless-steel
MRI-compatible flexible probe: SU-8 side protect, polyimide based, titanium as mask for SU-8

Don’t forget to check out http://m8ta.com/ (Tim Hanson’s article collections)