Steve
My zoom room: https://brandeis.zoom.us/j/7244456538
Today :
Priorities:
My zoom room: https://brandeis.zoom.us/j/7244456538
This week:
John Dowling talk notes:
Koomen and Wald: dark-adapted retinas go from purple to yellow to colorless (retinal)
dopamine inhibits gap junctions in horizontal cells, changes RF size
these dopamine amacrine cells in fish receive centrifugal projections from the central brain, presumably can adjust tradeoff between resolution / contrast sensitivity from the brain
John Dowling conversation: did retina evolve from pineal gland? also study with injection of AAV into retina: https://pubmed.ncbi.nlm.nih.gov/34031601/
Chat with Travis Massey -
Lawrence Livermore National Labs partners with investigators to fabricate polymide probes with many recording sites, similar to silicon probes but probes are flexible. Can be customized with many shanks and recording sites. The probes are some 30 microns thick. They require grant funding, and they have made arrangements with investigators for R21, R01, U01, U24, etc. The fabrication runs cost about $30,000; acquisition equipment costs about $15k (their users use SpikeGadgets), so about $50k needed in total. The electrodes are inserted by attaching them to a stiff silicon substrate with PEG, and then the PEG is dissolved with saline outside the brain and by CSF inside the brain.
SFN 2022:
talk to Allison Murphy about data
talk to Andor about cameras - did it, they are going to get in touch
Next steps: DID
The last thing is validation
SBIR
SBIR people: Taryn Aubrecht (talked to), also Annette Gilcrest
Sttr
Research partner - 40% 30% 30%
Does icorps disqualify us? No
Stir - can some labs testing a system work?
TABA - $6500
Named person
40%
Total cost
Waivers
Brain research tools
Make sure to write about commercialization.
Phase 2 outline
Grant help
Is it effective?
Receive payment
Sbir
3 times a year
January 5
Applicant assistant Eva garland consulting 1 page April
Phase 1 - $700k (NIDA only)
2 years
Commercial potential
Phase 2 - $3M, $1.5M
Commercialization plan
NIH seed
Assist
Carol L. Tompson at Allen knows how to get the data from BICCN: search visual cortex without BICCN checked
ONTOLOGIC - online computing center
NeuroConv - a conversion system for NWB
VIEWPixx - LCD that simulates a CRT, $15k (120 Hz CRT)
Neuroscience Associates Inc (NSALabs.com), can process 4 ferret brains for about $6000
Cambridge NeuroTech - RODIN head-fix system and electrophysiogy probes, maybe lower impedance than NeuroNexus
Compression of neurophysiology data: github.com/AllenNeuralDynamics/wavpack-numcodecs and flac-numcodecs
Metadata: Open Minds
Data re-use: Adam Ferguson et al 2013 , Syndromic space, paper title "The promise of data science" (Ferguson an author but Nielson first author)
Data Governence
Markiewiscz et al 2021 - reuse of data
Allen Brain and Dandi 100 datasets in 2022 and 20 in 2019 single digits in 2016
Code ocean -> development environment. Nextflow
Ute Hochgeschwender - The paper on the optical synapse I mentioned is at: https://www.nature.com/articles/s42003-021-02981-7
NeuroPixels:
€2800 acq
5x€1200 trodes
€200 cable
€200 headstagr
https://www.neuropixels.org/probe1-0
Mark histed preprint orawe
Shapley direction result
Feller macroscope
https://brandeis.zoom.us/rec/share/FRvdcnm5TEMAw2hgnBzTVNq4jWMz0T7YXL4BQmy8wRDHeMVf3P_oubE2xbTIXoTV.JUkQ3ja5aDN0Gamn
https://brandeis.zoom.us/rec/share/4xiy47RLsrPBV53pzQ7a_dk1IGA4sFN4GPwZxo03XM6UgqodRPeQjFD-fUuLIqMn.SSsUNTd2wo_7rxAr
https://brandeis.zoom.us/rec/share/MMpkft2WFzxd7YXvPhOvar3kegVWVZiPkkZUnraBgSSs3nLNEOMFQb9tVMg49x_l.FzBK4IHxN6OWGGKM
https://brandeis.zoom.us/rec/share/Jcq-xpe4Chs1I05ru2TYz4ckMoNRKDaSM8sTWSYgEdjiLIQ3AhvATHJs8uqDfus.H787KAuDojZgTFBo
Getferdi.com - link Slack, mattermost
Training Avi:
Zoey does:
Ordering
Hiring people
Ferret care
Lab jobs
Files
IACUC -> transfer ownership
Steve does:
Management page
Retina:
Interactions of vision and retinal waves
Plan A: In vivo
In anesthetized animals: can follow the same animal a few times
In awake animals: can follow the same animal daily, can see if early eye opening shortens or prolongs the period of spontaneous waves
Plan B: In vitro
2-photon, single cell and population
takes development, need to figure out how to make media, etc
one wonders if the results in vitro are a good mimic of the in vivo situation
UMass visit:
Ephrins: Hansen MJ https://pubmed-ncbi-nlm-nih-gov.resources.library.brandeis.edu/9883724/
Vikko
Me read speed papers
Select electrodes for physiology experiments
Hartley stimuli
Zoey
Eye tracker
NDI
Integrate NDR-matlab
Doc about contributing
JRClust tutorial
Get JRClust tests done
Submit to archive!
Example website: http://handbook.datalad.org/en/latest/index.html
Ideas from Daniel:
OTL - Innovation center
Peter Sawas
102A - COSI Entreprenourship
How to deal with files that have multiple epochs? We actually can't right now
Documentation - 20 minutes a day
Add multiple binary files ability to dumbjsondb
New version of markgarbage that uses appdoc
Rig stuff:
Display++ vertical retrace
sync for new 2-photon rigs
sync for new 2-photon stim computers
When hell rewarms:
Germany trip reschedule
2-photon changes:
analyze recorded data from new PrairieView
Array tomography
NeuroNexus matrix: $4250 (128 channel)
https://neuronexus.com/products/neural-probes/matrix-small-animal/
$2880 (64 channel)
Matrix Adapter kit - $400
https://microprobes.com/products/multichannel-arrays/mea
Experiments
Touboul - mapping, Shen/Dan/Zoey
Understanding Statistics and Experimental Design by Herzog, Francis and Clarke. Springer:
https://www.springer.com/gp/book/9783030034986
Variation in young vs old v f curves
FLIM - read Enrico Gratton
Management OKRs, Fall 2018
data structures for two-photon ROIs
imstream -> epoch and frame, size, channels (what about drift??)
intrinsic paper: https://www.sciencedirect.com/science/article/pii/S1053811901909504?via%3Dihub
Conversation with Carina Slidsborg
Glasgow Gordon Dutton
Cognitive visual impairment
visual maturation and development
visual delay
We use Art Optical as our vendor for ferret contact lenses. My contact there is Ruth Knight: rknight@artoptical.com
In the past we have ordered various parameters, ie diameters for the lenses 4.0 mm, 6.0 mm, 7 mm and 8 mm, Power: +2.0, +3.0 and +4.0 and base curvature 2.8 or 3.0. We've since standardized the size we use to the following ( based on preference as well as the inability of Art Optical to make certain diameters :
BC 3.0
Power +2.00
Diameter 6.0
Hope this info helps. We were quoted last at $92 per lens ( in December 2020).
Best,
Nicole
Multiple directory analysis of reverse correlation
Papers to go:
Biol107a survey data: how to represent multiple choice answers over time?
neural networks: attempts to stabilize by control theory (PID), where signal is deviations? (Multiple time scales, feed-forward inhibition, feedback inhibition, homeostasis)
Carbon fibers:
PEG P2139 Sigma 8000MW, little dots
Fiber supplier: Goodfellow USA
Jewler's vice: PROXXON
benchtop paralyne-C depositers?
Hirosci connectors
Michael Bruchas - optogenetic chips
RunExperiment 2 upgrade
bio107a coding problems:
breaking down into small, precise steps
SEEING the steps
Consensus clustering
Reading list: Dalva 2010, Erisir and Dreusicke 2005
Feldheim gradients
Brandeis: do we need a laser cutter?
spinal cord development
Anne Becker
Lynn Landmasser
multichannel analysis
Tim Hickey's student progress checker
Perusall NotaBene -- teaching tools
ask Sacha about Biol107a
Math Becci Torre
Can ask for consult from Karen Muncaster
Ione Fine's Matlab book
this week:
Intracellular analysis: add higher order reverse correlation?
Can we describe:
Width of RF, both in space, and in space-time?
Directional tuning of RF
What about showing that the cortex can learn spatial-temporal patterns with "teaching" that it cannot learn without teaching? Would broaden appeal. It would suggest that 1) a top-down teacher
Any evidence that horizontal connections influence the course of normal development?
Ocular transfer experiment indicates connections within cortex are important (though doesn't nail the fact that it is horizontal connections)
If long-range was important, then could see if long-range axons respect direction columns.
Or animals that have undergone normal experience should exhibit optical ChR2 direction tuning across the cortical surface. This seems like the most robust and easiest one. What about seeing it increase during visual training? If we did see this, it would be a very strong case. On the other hand, it might be small over a small interval, and might not involve the cells we have ChR2 loaded into.We don't have a prediction as to the magnitude.
shining on V2, what kind of pattern would be shown in V1
Gamma - moving forward, alpha moving backward Rolfsimmer lab http://www.pnas.org/content/111/40/14332.long
correlations: working speed of the local network, correlations coming through the inputs
top-down: feed-forward
feed-back alpha
V1 to V2
NSF:
edge solicitation - NSF - non-model organisms
team neuroscience - Jim Olds
theory hub - brandeis? is deadline gone?
Data: Marco Zarbin - https://pubmed.ncbi.nlm.nih.gov/34293094/
BRAIN meeting 2019:
Data interface and JRclist
INCF, data standards validation, mmartone@ucsd.edu, mathew@incf.org
Na Ji: FACED - use cylindrical lens and two mirrors that are at slight angle to each other, creates a beam in 1 dimension, can image by measuring FLIM because the photon delivery is offset in time
Diego Restrepo: 2-photon imaging with fiber bundle
adler a gan w 2019
Murakoshi H, Shin ME, Parra-Bueno P, Szatmari EM, Shibata ACE, Yasuda R.
Neuron. 2017 May 3;94(3):690. doi: 10.1016/j.neuron.2017.04.027. No abstract available.
http://learning-2-learn.github.io/panneuro_binder_demo
RCN NSF: Kurt
EM colabel fluorescence and EM Development of Genetically-Encoded Barcodes and Probes to Probe Neural Communication Under EM and Fluroscent Microscope
Speaker: Rongbo Sun, Yulong Li
optopatch - combine with ontogenetic stimulation to detect E/I
Azadeh Yazdan-Shahmorad -> stimulation to reconfigure cortex
Melosh Stanford
Cindy chestek Michigan
Histology:
Other items:
*=pushed as far as I can right now
two populations of animals: measure KL, DS, etc.
alpha gamma
dendritic imaging: Can we image lgn inputs onto layer 4 cells
Tutorial for single unit analysis
Tutorial for single unit acquisition
Phase
Screen size
Number of cycles
Acquisition list
Rigs:
Analysis:
Analysis of reverse correlation with multiple stims
ON/OFF separate analysis
Testing with model cells
Which is the best method?
R = [D*s - L0]^N
R = [D*s + STC_filters]
R = [OFF + ON]^N?
Documentation:
2-photon analysis
add to database should let you select the directories to add
NewStim explanation
Spike2 spike sorting documentation
LabView documentation
Visit w/ Beggs: W. Maass, Reseviour computing, Echo State Networks (in CS), Liquid State Machine (in Neuroscience). Bertschinger, Natchlager, Neural Computation, 2004?
breadboard - can also use prototyping circuit board
ideas:
possibly run Wyeth's stim in developing ferret?
tecoflex
Lubrizol; Thermedics Polymer Products, 207 Loewll St., Wilmington MA 01887. The catalog number seems to be EG-93A (0101260870)
Short term:
8) Rotation projects
Mouse imaging
Pattern of fractures in direction maps with respect to orientation / retinotopic maps http://www.ncbi.nlm.nih.gov/pubmed/?term=Tsodkys+direction+orientation prediction that orientation/direction domains will be elongated in the direction of optimal movement
Programming for 2-photon image analysis
Fast scanning
Re-targeting XYZ
(Sort of already have this.)
Effective scan patterns for dealing with drift/signal-to-noise issues
This scan pattern should allow us to correct XY drift, and to detect bad Z drift to ignore data
Wiener filtering
Hardware: Carbon fiber electrode making
Software:
If experienced:
Linescan data analysis
If inexperienced:
Liam Paninski - implementing spatio-temporal demixing?? Pnevmatikas et al 2013 Vogelstein Paninski
Virus design
Shift work on electrophysiology
Aligning injections and slices
Staining slices for immuno
Trying to make correspondences between in vivo/in vitro
Looking at coronal slices, trying to figure out where one is
10) ideas: AT or VGlut staining for examining development of layer 2/3 cortico-thalamic connections?
NSF ideas: Campus Cyber Infrastructure -- upgrades for networks and computing
That silicone stuff for molding that Jenn brought in once: Sugru
EB 2016:
Generation of Functionally Distinct Projection Neurons in the Mammalian Neocortex. U. Mueller. The Scripps
Res. Inst. Several types of progenitor glial cells, one type expresses Cux2 (apparently produces upper layer neurons)
Spinal cord session: Start and Stop: A Matter of Excitation. O. Kiehn. Karolinska Inst.
notice this twice: recording axonal responses from silenced cortex to look at STRF of thalamic input (Chapman 1991??)
TNFalpha blocker virus to turn off homeostatic plasticity at eye opening (developmental problems, might be doing something before eye opening); also, doesn't this inhibit only 1 direction of homeostatic plasticity?
Are horizontal connections capable of altering receptive fields?
Are horizontal connections altered by visual training?
Nikon - Nicholas Deakin, ndeakin@nikon.net
SFN 2019:
International brain lab has nice stereotaxic frames for 2-photon imaging in mice
Ben Hayden might be interested in NDI, maybe Stephen Shepherd
Person to invite for Comp J Club: Mark Harnett
Nightsea fluorescent illuminator adapter
People to search for at SFN:
Fitzpatrick
Swadlow
Sur
Alonso
Hengen
SFN 2018:
Carbon fiber processes: Massey Carmena lab
Form2 can print carbon fiber jigs if you orient them such that the high resolution dimension of the printer matches the high resolution dimension of the jig
Carbon fiber: make the silver print even more runny, Keith thinks it may shoot out because it is too viscus
Betsy is the carbon fiber expert in Keith's lab
Microwire electrodes: Neurotrodics MCI is distributer
Open source software: OpenEphys
International Brain Lab
Direction-selective input onto non-direction-selective inhibitory interneurons in V1 of rabbit - Swadlow (no detected input to E cells)
B-I Bae interested in making genetically-modified ferrets
SFN 2017:
Stages of neural polarization: 1 little things, 2 slightly longer, 3 one process longer, 4 one process significantly longer with a cone, 5 axon and dendrites
Rumpel simon red nuclear staining with gCamp
Matt Colonnese - spontaneous activity
Francesco Tamagnini <f.tamagnini@reading.ac.uk> - visual to perirhinal connectivity
Jeff teeters datacite GitHub
Senso medical contract fab
Nero - neural data organizer?
Crcns 2 proposals?
T-bolts for ferret head posts
Prereview.org
Authorea citation thing
UCLA multichannel electrodes
SFN 2015:
Plexon U probe: 24 tightly packed channels ($5300 each, can be re-used many times)
Phy.cortexlab.net - massive spike sorting effort
IMEC probes - 900 channels (approx)
Damian Wallace - squirrel eye movements??
Swartz 2014: virtual finger, tracing neurons
SFN 2014:
Jose suggests U probe for dense lgn recordings
Company called "Aims" has small stereotaxic light
Read papers by Roland PE (voltage sensitive dyes)
Doric lenses has Schnitzer scope like thing
SFN 2012:
Drive through artificial dura? Anna Roe makes thick artificial dura that one can drive electrodes through, and perform imaging through, but it has to be molded in advance.
What kind of dura did Todd use?
Computar is a good lens company -- maybe go back to multichannel systems to find their specific lens
Good small camera: UEye UI-1550LE-C, Computar lens MLM-3XMP
Nice, small magnetic bases: http://www.kanetec.com/products/featured/mini_magbases.shtml
nDrive from NeuroNexus -- coupon for 20% order of $1000 is XKSA119
You-3 small manipulator from Narishige
Read Mante et al. Newsome
LGN papers to read (Bonin): http://www.ncbi.nlm.nih.gov.resources.library.brandeis.edu/pubmed/18498742
http://www.ncbi.nlm.nih.gov.resources.library.brandeis.edu/pubmed/16306397
2013 ARVO
Cool looking lenses, www.ocularinc.com
Accounting terms:
pro-forma statement - invoice and billing before shipping
Shon et al. 2004
Experiment 1:
Feedforward E+I, but I delayed
I constant across space
E weights develop spatial asymmetry
Predicts untuned inhibition
Velocity tuning is poor, doesn't match (unless we imagine that the inputs are velocity tuned, which they are a bit)
Experiment 2:
I competition, veto; null direction inhibition
Experiment 3: waves across horizontal surface
Anticipatory signals??
2017 Teaching and Learning Institute (Brandeis)
1st day, introducing people sitting next to me:
Sava Berhané (Leadership, Biz 10a, implementing argumentation and writing, prompts, case based class, case method)
Bill Wllet - Management and Communication course, involving writing, argument, presenting. Lots of case studies. Wants to learn to use prompts, peer feedback in writing assignments before submission, etc
Teaching techniques:
"cough test" to indicate agreement
Doug Kirshen - dkirshen@gmail.com - teaching freshman composition, wants writing examples
Brainstorm: writing exercise:
Divide paper into 3 columns: literal writing, "reader energy", and "reader thoughts" (thought: should reader energy be a color?)
Reverse outline: divide paper into two columns: literal (what is written) and meta (what is the reader thinking)
Have students read a stack of papers to understand the burden of reading, and reader energy
Bio107a issues
teamwork: freerider problem, work hog problem
solutions: give materials on creating effective teams, tell roles, tell them they'll be fired if they don't do their jobs
1 on 1 meetings -- short code problem -- how is it going?
Funding ideas: Alkermes funding 2-photon work?
Tank lab
Dombeck and Tank 2007, 2009, 2010
has information on head plates, imaging stablizing, optical windows for 2-photon imaging in mice
Good dental cement is Metabond (also from Tank)
Viruses
Good contact: Botond Roska, MD, PhD
AAV info:
Sc aav, self-complimenting AAV has very fast expression but half the package size of other aavs
strains 6 and 1 aav are excellent at being transported in a retrograde fashion
Botond says he thinks 1 injection of a cre-based AAV and a Cre-dependent AAV would work
Talk to Ed Callaway about what they've tried
Choi et al 2010
Translation outside of floxed sites makes transcription work better
Genetically-encoded calcium indicators:
Yellow chameleon aav.-hsyn-yc3.60
Stable over time
Comparison of genetically encoded calcium indicators: chameleon 2.60 is better for a wider range of spikes (816.21)
Multichannel positioners
Alpha-omega 8 chAnnels independent moves $22
Optics:
Optoma pico 102 ptwyford@ufl.edu small DLP projector
Optical fiber insertion in brain:
www.doriclenses.com
Branka prijovic Branka@doriclenses.com
Openoptogenetics.org
Reorganization of cortical dendrites/axons project with Sue's lab:
Thalamic Axons rewire after 24 hour MD
PARs - genes that regulate polarity
ephrins - do they persist?
repulsion? self-repulsion?
ThorLabs:
Will send dichroic filter wheel - christian johns cjohns@thorlabs.com 973-579-7227
$70k confocal
RF mapping experiments:
Reid direction papers
Movshon tolhurst
Imaging technology
silicone from Kristina:
We are currently using this stuff from Shin-Etsu to make artificial duras: KE-1300T/CAT-1300
Link to their webpage: http://www.shinetsusilicones.com/shindex.html
You can request a sample through their webpage, but that didn’t work for us. Instead Erika called them and convinced them to ship us a sample. We haven’t fully tested it yet, but Xiaoqin Wang’s lab used it in one marmoset and was quite happy with it.
Things I like:
how circuits work: how the connectivity and intrinsic properties leads to responses; how these might be edited by sensory experience; fine control over the stimulus and ability to observe the responses
What about cell types? The only animal where one can manipulate cell types specifically is the mouse
Everyone and their brother is doing this, what could I add?
Things I like:
how circuits work: how the connectivity and intrinsic properties leads to responses; how these might be edited by sensory experience; fine control over the stimulus and ability to observe the responses
What are the major response properties in visual cortex: orientation tuning, direction tuning, surround suppression, normalization
Orientation tuning and spatial frequency tuning break down in amblyopia -- why? is it loss of one class of synapses (such as ON) or is it just a general degradation of synapses?
Development of ON/OFF channels
How much would it cost to get preliminary data?
I would have to go to David's lab for a month to get the data because we'd need people to feed the shrews and an incubator
Could you NOT do it in ferret?
Would need to record RFs in layer 4
What about thalamocortical axons? Would need to inject LGN with high concentration ChR2 and see if we could get the axon to grow..could do it in mouse
Broader Impacts, Vivek:
Summer program: paired high school students w/ grads, postdocs
Had 2 courses, 90 minutes in duration each: one of them involved reading papers, science literature, writing papers; the other involved life journey and discussion
Participants were 70% URM, 70% female cases: Sejal - now UG working for Leslie, has a paper, William, now UG working for Michael, has paper
New 4 credit course at Waltham High School: 24 juniors and seniors interested in science.
Modules: Intro (data, regression, stats), Environment (citizen science, science literature, plants), Augmenting Humans, Psychology and depression, physics and universe, maybe SciBiz