Hot task list

Today :


My zoom room:

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:

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 people: Taryn Aubrecht (talked to), also Annette Gilcrest


Research partner - 40% 30% 30%

Does icorps disqualify us? No

Stir - can some labs testing a system work?

TABA - $6500

Named person


Total cost


Brain research tools

Make sure to write about commercialization.

Phase 2 outline

Grant help

Is it effective?

Receive payment


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


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 (, 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: 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:


€2800 acq

5x€1200 trodes

€200 cable

€200 headstagr

Mark histed preprint orawe

Shapley direction result

Feller macroscope




  • - link Slack, mattermost

Training Avi:

Zoey does:

  • Ordering

  • Hiring people

  • Ferret care

  • Lab jobs

  • Files

  • IACUC -> transfer ownership

Steve does:

  • Management page


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


Me read speed papers

Select electrodes for physiology experiments

Hartley stimuli


Eye tracker


Integrate NDR-matlab

Doc about contributing

JRClust tutorial

Get JRClust tests done

Submit to archive!

Example website:

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)

$2880 (64 channel)

Matrix Adapter kit - $400


Touboul - mapping, Shen/Dan/Zoey

Understanding Statistics and Experimental Design by Herzog, Francis and Clarke. Springer:

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:

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:

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).



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

correlations: working speed of the local network, correlations coming through the inputs

top-down: feed-forward

feed-back alpha

V1 to V2


edge solicitation - NSF - non-model organisms

team neuroscience - Jim Olds

theory hub - brandeis? is deadline gone?

Data: Marco Zarbin -

BRAIN meeting 2019:

Data interface and JRclist

INCF, data standards validation,,

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

Kinetics of Endogenous CaMKII Required for Synaptic Plasticity Revealed by Optogenetic Kinase Inhibitor.

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.


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


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


Screen size

Number of cycles

Acquisition list



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?


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


possibly run Wyeth's stim in developing ferret?


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 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


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,

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:






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 <> - 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

Authorea citation thing

UCLA multichannel electrodes

SFN 2015:

Plexon U probe: 24 tightly packed channels ($5300 each, can be re-used many times) - 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:

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):

2013 ARVO

Cool looking lenses,

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 - - 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)


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


Optoma pico 102 small DLP projector

Optical fiber insertion in brain:

Branka prijovic

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?


Will send dichroic filter wheel - christian johns 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:

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