brain initiative notes

biafra ahanonu


updated: 29 November 2015 | started: 20 May 2013
biafra ahanonu

This is a collection of news, ideas/findings, and other tidbits related to the BRAIN initiative, promising (bio)technologies, and topics related to neuroscience/biology research in general. Keep up-to-date via the brain initiative notes rss feed.

Currently obtaining my PhD in Mark Schnitzer's lab at Stanford University and can be reached at bahanonu [at] stanford.edu.

My main website is located at bahanonu.com

Usage notes


introduction (hover/click to expand)

Goal: A healthy debate is currently afoot in neuroscience as to what we will ultimately gain from developing and using various technologies, how to analyze and store the mountains of data, and other questions. This is my collection of ideas, findings, and other tidbits related to the recent BRAIN initiative announcement, promising (bio)technologies and neuroscience in general that aim to find answers to questions being raised. This is an exciting time in neuroscience, I hope to convey that here!

Notes: As a living document, I’ve labeled entries with [draft] if they are not completed; they are posted here as food-for-thought and will be revised and finished after further research, modeling, and/or experiments. Anything with [#] is a reference link to the bibliography at the end of the document. Footnotes are indicated by a superscripted number and are also located at the end. The index provides a convenient place to find concepts, names, and other terms sprinkled throughout the text.

Code: This document was compiled using htlatex. A template for converting LaTeX to html (as I’ve done here) can be found on my latex boilerplate github repository. I use Lazy Load to reduce bandwidth associated with loading the page (images are only loaded if the user views them).

Thanks: Tom Dean organized a superb class at Stanford—cs379c—that pushed me to probe developments in neurotechnology in greater depth. He has an excellent set of notes on the topic as well.


table of contents (hover/click to expand)

Contents

sources of information
    blogs
    books
    businesses
    conferences
    database
    fabrication
    grants
    journals
    journal volumes
    labs
    lectures
    literature search
    news
    optics
    programming
    programs and institutes
    resources
    statistics
    viral resources
2015.11.19
 New voltage sensors: Ace2N and Ace1Q
2015.10.30
 Society for Neuroscience 2015 notes: pain and reward circuitry
2015.10.22
 Society for Neuroscience 2015 notes: pain technologies
2015.10.11
 dual photo-stimulation and imaging, review
2015.09.27
 Science is hard
2015.05.11
 Lighting the brain with optogenetics
 Rigor and reproducibility in scientific research
2015.05.08
 Working with and sharing large datasets, part 1
 optoXRs
2015.04.30
 3D CAD modeling of mouse surgeries
2015.04.22[draft]
 editing the human germline
 increasing science funding
 circuit reconstruction
2015.04.19[draft]
 taking care with statistics
 EMBO Drosophila workshop
 Women in science, part 1
2015.04.18[draft]
 Glial uptake of neuronal huntingtin
2015.04.16[draft]
 Do incentives work?
2015.04.02
 Philosophical Transactions B review issue
 Neuroscience Initiatives
 Defining consciousness
2015.03.28
 trans-generational transfer of traits or Lamarck revisited
    Reviews
    Articles
2015.03.26[draft]
 Non-invasive stimulation of neuronal activity
 ACC + DR pain
 pain general
 looking at grants
2015.03.20
 Creating reward memories in the hippocampus
2015.03.18
 Highly cited papers
 From circuits to behavior
2015.03.15
 Significance testing
 Miniature microscope and fiber photometry mini-review
2015.03.12
 SCAPE and other microscopy
 Automatic detection of touch stimuli
 Puzzle imaging?
2015.03.08
 Fundamental limits of computation
 New mice from Allen Institute
2015.03.03
 3D imaging of zebrafish
2015.02.28
 Advances in artificial intelligence, part 2
2015.02.19
 On publishing about what we already knew
 Imaging axon activity with SyGCaMP
2015.02.14
 The trend towards funding older investigators
 Imaging neural activity in 3D
 Determining anatomical locations or how well does animal work replicate human physiology and brain activity?
2015.02.12
 GPS tracking in bats
 Improving PCA-ICA for cell detection in calcium imaging
 Human Brain Project
2015.02.11
 Virtual reality and BMI
 On writing well
 Photonics west
2015.02.01
 Investigating hypothalamus activity with the miniature microscope
2015.01.30
 Advice for starting graduate students: choosing a lab
 Advice for starting graduate students: being successful
2015.01.29
 Does science require experiments?
 Photoactivatable neuropeptides
2015.01.28
 Connectome
 Haruhiko Bito talk
 Science magazine issue on ESA’s Rosetta mission
2015.01.22
 Gyorgy Buzsaki talk
 dual photostimulation and optogenetics
2015.01.20
 10,000 bit word computers
 Theoretical neuroscience issue
 opto-fMRI
 Ecological expected utility and the mythical neural code
2015.01.18
 Human optogenetic trials
 Another look at the Turing Test
2015.01.16
 automating medical health records
 random person to know: David Hilbert
 linguistic relativity
 ultra fast imaging
2015.01.14
 high throughput screening of C. elegans
2015.01.12
 the stress of biomedical research
 3D place fields in bats
 random cancer
2015.01.10
 physicist view of the world
 viral tropism
2015.01.08
 freely moving two-photon imaging
 Bongwoori, a new voltage sensor
 imaging multiple brain regions
 China
 microcontrollers
2015.01.06
 optogenetics identification of single unit recordings
2015.01.05
 optogenetics and pain, continued
2015.01.04
 advances in artificial intelligence
 artificial intelligence and the law
 curing Alzheimer’s?
2014.12.24
 astrocyte imaging
 voltage imaging, screening for better probes
 single cell analysis
2014.12.22
 dual photo-stimulation and imaging, cont’d
 dual photo-stimulation and imaging, update
2014.12.18
 neuroscience foundations and institutes
 using stem cells to treat eye degeneration
 CaMPARI update
2014.12.15
 new miniature microscope papers
 freely moving dual photostimulation and imaging
 wireless sensors for monkeys
2014.12.13
 using microprisms to access hard to reach brain areas
2014.12.03
 some interesting papers/articles
 managing the paper overload
2014.11.30
 neuroscience technologies
2014.11.29
 doric miniature microscope
2014.11.28
 rebuttal of the trillion odor hypothesis
 3D Light Field Microscopy
2014.11.23
 dual photo-stimulation and imaging
2014.11.22
 presenting scientific research
2014.11.20
 simultaneous imaging in multiple brain regions
2014.10.06
 Nobel prize goes to identifying brain regions involved in spatial navigation
 GCaMP6 reporter mice
2014.09.30
 NIH BRAIN awards
2014.08.22
 large scale imaging and other papers
2014.08.17
 limits of neuroscience
 on interstellar travel
2014.08.16
 limits of computation
 designing brain-based computers
2014.08.13
 circuit reviews
2014.08.11
 list of pharmaceutical company projects
 connectivity tracing
2014.08.10
 recent papers
2014.07.11
 scientific impact
2014.06.28
 more CLARITY
 Cell now publishes letters
2014.06.22
 statistics: effect sizes
 spike metrics
 more CRISPR
 physiological optogenetics
2014.06.08
 drug industry productivity
 consumer virtual reality
 from the archive: some interesting papers
 from the archive: dendritic computation
2014.06.03
 wireless recording from freely moving monkeys
 causal investigation of memory and LTD/LTP
 spatial optogenetics
2014.06.01
 updated RSS feed
 papers from 9.29
2014.05.31
 unique author identifiers
2014.05.29
 biological logic and computation
    boolean logic in bacteria
    learning in culture
    connectivity and weighting
    patterning circuits in vitro
2014.05.27
 persistent homology
2014.05.25
 DREADDing feeding
2014.05.24
 whole animal 3D imaging
 optical clearing
2014.05.21
 AstraZeneca’s pipeline
2014.05.12
 computational neuroscience papers, part 1
2014.05.08
 new neuroscience tools from janelia
    calcium sensors
    neurotransmitter sensors
    dual fluorescence and EM imaging
    imaging fine processes
    calcium integrators
    designed genetic switches
    GWAS 2.0
2014.05.07
 anti-aging brigade
2014.04.25
 improving optogenetic silencing
 using FISSEQ and neuronal barcoding for connectomics
2014.04.24
 high throughput screening for neural mechanisms of behavior
2014.04.23
 grant funding, scientific impact and resource allocation
2014.04.22
 CUBIC: another clearing technique
2014.04.20
 SwissTech Convention Center
2014.04.19
 computational neuroscience resources
2014.04.13
 photoacoustic imaging
2014.04.06
 calcium imaging cell detection techniques
2014.04.05
 recording from 512 signals
 
2014.01.02
 anti-aging
2013.10.29
 NeuralMapper
 cortical column organization
 data organization
2013.10.22
 the mouse nervous system
2013.10.09
 optogenetics and pain
 recent tech
2013.09.27
 papers
 CRISPR
2013.09.14
 ethics of science
 from the archive
 random topic
2013.09.10
 brain initiative
 just plain cool
 neuroscience
 Drosophila
 CRISPR
 biology
 from the archives
2013.09.05 [draft]
 nitrogen-vacancy diamond centers
 tracking changes over time
2013.09.04 [draft]
 computational inference of the known unknowns
 from the archives
2013.09.03
 tech articles
 from the archives
2013.09.02
 ASBMB report
2013.09.01
 articles
 from the archives
 just plain cool
 sites
2013.08.25
 articles
 from the archives
2013.08.22
 towards an integrated science
2013.08.21
 useful links
2013.08.19
 brain machine interfaces
2013.08.18
 recording/decoding neuronal populations
 bonus papers
 terahertz
2013.08.13
 neuro-papers
2013.08.12
 various papers and links
2013.08.05
 keeping up with the literature
2013.07.31
 wireless optogenetics
2013.07.28
 arvix paper
2013.07.27
 basic BRAIN research
2013.07.26
 false memories
2013.07.25
 Phonon lasers
 statistics of molecular ticket tape
 functional tracing of neural projections
 connectivity review article
2013.07.23 [draft]
 CRISPR and TAL Effectors
 optogenetic gene control
2013.07.22 [draft]
 Neural Dust
2013.07.19
 nature BRAIN opinion piece
2013.07.18 [draft]
 The Human Connectome
2013.07.12 [draft]
 nano detection of cellular activity
2013.07.11 [draft]
 scalable neuroscience paper
2013.07.08 [draft]
 parallelization: to CUDA or not?
2013.07.04
 sources of information
2013.07.02 [draft]
 nanoscale thermodynamics
2013.07.01 [draft]
 SeeDB: new clearing method
2013.06.30 [draft]
 physics of BRAIN
2013.06.29 [draft]
 light sheet microscopy and CLARITY
2013.06.26 [draft]
 memory transfer
2013.06.20 [draft]
 dealing with big data
 neuronal activity
2013.06.14 [draft]
 expanding the molecular ticket-tape
2013.06.09 [draft]
 miniaturizing sequencing
2013.06.06 [draft]
 excreting a DNA encoded brain signal
 the costs of brain diseases
 gaming, google glass, and neuroscience
2013.06.04 [draft]
 function of microcircuits
 the connectome
2013.05.30 [draft]
 memory transfer
 maintaining an external human brain
 correlation between brain power and neuron number
2013.05.29 [draft]
 science fiction to sell the vision
 genetically encoded nanotechnologies
 number of transistors needed to send a signal
 estimating technological integration
 genetically encoded contrast agents
2013.05.27 [draft]
 placozoa and marine neuroscience
2013.05.24
 optical readout of brain data
 analysis of brain data
 tardigrades
 equation test
2013.05.23
 brain projects across the pond
 simulating neural systems
2013.05.22
 mining the visual system for algorithms
 analyzing brain data
 neurons and glia
 power analysis in the brain
2013.05.20
 analyzing OPIDs for brain readout
References
Index
Footnotes

List of Figures

(right) Ace2N and Ace1Q voltage sensor constructs and example cells. (left) Example optical (top) and electrical (bottom) trace from the same cell.
Epidural optic fiber implant for spinal optogenetics
Anna Poon wireless delivery to mice
An Optogenetic Demonstration of Motor Primitives in the Mouse Spinal Cord
Optogenetic control of aversive sensory circuitry
Overview of current technologies and protein systems used for recording from and manipulating neurons.
A visual representation for one method of storing multi-dimensional, ever-changing biological data.[76]
microCT of a rat head with blood vessels.
Based on human and other data, there seems to be a stereotyped progression of neuropathological changes in neurodegenerative disorders that are thought to be caused by spreading of protein aggregates.
10 Illustration of Drosophila olfactory bulb and glia nearby. HttQ are the versions of huntingtin used in the study to investigate whether glia are uptaking them.
11 Overview of Integrated information theory’s ability to predict which systems can have experiences.
12 Description of transgenerational epigenetic inheritance.
13 left TRPV1 is a heat/capscacin responsive receptor whose activity is altered by magnetic nanoparticles that are heated when a magnetic field is turned on. right example calcium influx in response to application of a magnetic field (see bottom left subpanel).
14 Protocol for inducing reward-related memories tied to a specific place by activating reward centers when place cells fire during sleep.[16]
15 The panel on the left (from the paper discussed below[49]) is meant to show the increased interest in amygdala research. It does not. When you compare to the number of articles published overall, see right panel, it becomes obvious that this is due to an overall increased output in overall academic research publications.
16 Miniature microscopes and fiber photometry for measuring neural activity.
17 Example of SCAPE microscopy, which both projects and images a plane of light in a sample through the same objective.[4]
18 Laminar optical tomography works by measuring the diffusion of light through a medium to nearby points. This can be used for volumetric reconstruction of images.[43]
19 As chips get smaller, they approach atomic limits, which leads to fundamental constraints on how densely packed CPUs can be with transistors while still being operational.
20 More mice!
21 3D imaging of a zebrafish heart.[75]
22 Demonstration of how electrically tunable lenses work.
23 Example of an artificial neural network used to play Atari games from [79]
24 What happens when artificial intelligence doesn’t interpret incoming data in an intelligence, generalized manner. One of the largest intra-day drop in DOW history.
25 Left: optogenetics paper from 2015[50]. Right: rat stimulation paper from 1982[100]. Both demonstrate that the SCN can influence circadian cycles by stimulating it (blue shared region in left, arrows in right image).
26 The average age of NIH investigators under 36 years old continues to decline.
27 Several ways to do volumetric imaging.
28 Example of GPS tracking in bats.[29]
29 Concept photo for Microsoft’s HoloLens.
31 Setup for imaging 1011 frames per second.
32 High throughput screening of C. elegans.
33 Comparison of spherical vs. toroidal systems for encoding bat’s position and orientation in space.
34 Comparison on a biologist’s (A) and engineer’s (B) view of how a radio works, from a physicist perspective.
35 One configuration for two-photon freely moving imaging.
36 A nice overview of molecular and cell biology related institutions in China and when they were founded.
37 A setup to allow optogenetic identification of single units during tetrode recordings.
38 EP2 pathway can have a number of downstream effects.
39 Setup for dual photostimulation and imaging in Packer, et al. 2014.[85]
40 left, from Adam’s paper (supplementary figure 1) measuring the probability of a spike on off-target neurons as a function of distance from photostimulation spot. middle, similar as left (supplementary figure 5), only with increase numbers of photostimulation spots. right, from Tank paper[95] (figure 3c) showing evoked responses as a function of distance from illumination spot.
41 left, stimulation by dendritic processes.[84] right, out-of-focus channelrhodopsin excitation.[96]
42 Cells expressing CaMPARI show different ratios of red/green depending on their activity at the time UV light was shone on the zebrafish.
43 Outline of research experiment using the miniscope to test effects of Zolpidem on neural activity.
44 Skematics for accessing mPFC and MEC using microprisms.
46 Doric flyer from SfN.
47 Two mixtures can share a different number of individual odors. This can be used to probe the number of odors a system can distinguish.[8]
48 The rebuttal points out that there is a distinction between sensory precepts being different from their nearest neighbors and being truly unique throughout the precept space.[73]
49 Setup for dual photostimulation and imaging of individual neurons.[95]
50 A classic experimental setup to directly test the necessity and sufficiency of neuronal activity observed during a behavior.
51 Richard Feynman during one of his.
52 The end goal is to avoid producing slides like this ().
53 Imaging setup from recent paper proposing a large field-of-view two-photon microscope.
56 microcircuit structure and computations
57 mouse connectome project overview.
58 Model of motor neuron recruitment during different stages of swimming.
59 The h-index during academic careers.
60 Break down in citation predictive power for highly cited papers.[116]
61 Aspects of the CLARITY workflow.
62 wireless recording from monkeys
63 protocol used in the paper, ODI is optically stimulation.
64 Angled optogenetic stimulation.
66 glutamate sensor
67 restoration of aging cells by parabiosis
68 bistable optogenetic silencing of neurons
69 experimental design
70 new CUBIC clearing technique outline.
71 an excuse to have a conference in switzerland
72 setup for photoacoustic imaging.[69]
73 performance of NMF vs. PCA-ICA.
74 determining connectivity via high density probes.
75 example of the imaging system.)
76 USA federal R&D spending.
77 Human control of rodents.
78 Inducing false memories.
80 Small neural dust sensing nodes placed within the brain can be powered from outside.
81 Detecting intracellular pressure with silicon chips.
82 
83 vision for creating a generalized parallel computing platform.
84 Analyzing thermodynamics at the nanoscale.[46]
85 New method for clearing brain tissue.[55]
86 Different methods of obtaining neuronal data.[71]
87 OpenSPIM setup.
88 An example of the advantages that can be gained from looking for redundancies in large datasets.[67]
89 Cost of sequence DNA has fallen drastically in recent years.
90 Use error-prone DNAPs to encode activity in DNA sequences.
91 Nonribosomal peptide synthesis
92 One possible way of multiplexing on a probe, this particular one delivers drugs and detects electrical signals.
93 The costs of various diseases. Error bars are variations in source data. This is not comprehensive as i am still finding more and better sources.
94 Science fiction of old helped inspire generations of engineers, we should do the same for neuroscience.
95 Using molecular imprinting with nano-devices.[9]
96 Anatomy of a placozoa.
97 Example OFDM circuit
98 Modeling leech movement circa 70s
99 Example of the CLARITY technique in action, it allows viewing of stains in the brain without the need to slice it into many sections, potentially allowing for better localization of proteins, etc.

sources of information (hover/click to expand)


sources of information [link]

Finding information on the cutting edge often requires wading deep in the primary literature. For this i turn to a variety of journals and resources, most of which allow me to discover articles that seem interesting or with possible applications in neuroscience. While summaries by journalists are often useful for getting a bit of history and other layman interpretations, it is often better for one’s understanding to dive right into the publications, reviews, and articles.

Below is a list of sources that are useful for staying up-to-date. It is by no means comprehensive and will be continually updated. Suggestions welcome!

blogs

books

businesses

conferences

database

fabrication

grants

journals

journal volumes

labs

lectures

literature search

news

optics

programming

programs and institutes

resources

statistics

viral resources


2015.11.19 [link]


2015.10.30 [link]


2015.10.22 [link]


2015.10.11 [link]


2015.09.27 [link]


2015.05.11 [link]


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2015.04.30 [link]


2015.04.22[draft] [link]


2015.04.19[draft] [link]


2015.04.18[draft] [link]


2015.04.16[draft] [link]


2015.04.02 [link]


2015.03.28 [link]


2015.03.26[draft] [link]


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2015.03.08 [link]


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2013.10.29 [link]


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