karel svoboda
@svoboda314
Followers
8,218
Following
468
Media
25
Statuses
318
Explore trending content on Musk Viewer
Marcellus Williams
• 568237 Tweets
Missouri
• 323410 Tweets
Supreme Court
• 283383 Tweets
River
• 157483 Tweets
Ghost of Yotei
• 86618 Tweets
Quito
• 62741 Tweets
Alex Jones
• 46651 Tweets
Vidal
• 40428 Tweets
アルシュベルド
• 39880 Tweets
Colo Colo
• 39045 Tweets
#TEN_Nightwalker100MSpotify
• 36304 Tweets
Lunar
• 35094 Tweets
Mets
• 33437 Tweets
9PP FANMEET PRDAY
• 33247 Tweets
Correa
• 29473 Tweets
#WWENXT
• 27211 Tweets
保険証廃止
• 22444 Tweets
Braves
• 22222 Tweets
#DWTS
• 17587 Tweets
Nacho
• 17504 Tweets
Borja
• 16781 Tweets
Royals
• 16471 Tweets
Colidio
• 15947 Tweets
#新ドリンクは和栗モンブランとチョコ
• 14958 Tweets
Palacios
• 14424 Tweets
モンハン
• 13103 Tweets
Astros
• 12294 Tweets
Excited to launch the new Allen Institute for Neural Dynamics (). We are a multidisciplinary group of scientists & engineers organized to understand how brain-wide neural circuits perform the computations underlying flexible behavior.
21
126
815
Wonderful news: Allen Institute announces Rui Costa as next President and Chief Executive Officer -
16
54
444
Excited about our long-brewing paper exploring dynamics in multi-regional neural circuits in a delayed movement task. Driven by
@esthersselva
,
@yiliu021
, and including Jennifer Colonell, Nuo Li and
@ShaulDr
and others (the MAP collaboration): (1/7)
5
110
333
A bit more unpacking:
jGCaMP7s - sensitive detection of activity
jGCaMP7f - more sensitive replacement for GCaMP6f
jGCaMP7b - higher baseline fluorescence, for imaging small structures (neurites)
jGCaMP7c - very low baseline fluorescence, for side-field imaging
New jGCaMP7s, jGCaMP7f, jGCaMP7b, jGCaMP7c green calcium indicator constructs sent to Addgene. Sensitive, fast, bright, and high contrast indicators. Characterization data (). Stay tuned for DNA & AAV availability ().
4
122
186
1
172
279
Something for everyone:
jGCaMP7s - sensitive detection of activity
jGCaMP7f - more sensitive replacement for GCaMP6f
jGCaMP7b - higher baseline fluorescence, for imaging small structures (neurites)
jGCaMP7c - very low baseline fluorescence, for side-field imaging
2/2
5
109
265
Some thoughts on rabies virus for tracing neural connections; a perspective from barrel cortex neural circuits ( ).
10
114
225
Are you a scientist with deep expertise in computational and theoretical neuroscience, with an interest in linking neural computation and neural dynamics in the context of defined neural circuits? Join the Allen Institute for Neural Dynamics ().
1/2
4
90
189
1/4 Comparison of population dynamics based on ephys and calcium imaging in matched neurons in behaving mice. Do imaging and ephys report the same thing? ; fun collaboration with
@ShaulDr
@TsaiwenChen
@zq_wei
& Bei-Jung Lin & Kayvon Daie
1
80
181
New preprint from the lab: A midbrain - thalamus - cortex circuit reorganizes cortical dynamics to initiate planned movement (). Work led by Hidehiko Inagaki and
@esthersselva
. 1/4
2
42
172
The Allen Institute for Neural Dynamics is recruiting for an exciting project on multi-regional neural computation. Recent PhD / MD, experience with extracellular ephys, strong quantitative skills, and interest in team science.
0
93
164
The Allen Institute for Neural Dynamics is searching for a Dir. of Sci. Computing (). Interested in i) extract discoveries from large-scale brain imaging and neurophysiology data; ii) building an agile team; iii) open science & software? Get in touch!
2
96
157
Benchmarking eight methods for optogenetic inactivation of brain regions using extracellular electrophysiology. ;
#bioRxiv
1
52
145
Are you interested in neural computation and neural dynamics in the context of defined neural circuits? The Allen Institute for Neural Dynamics is recruiting leaders for a program in systems neuroscience and behavior (; ).
2
56
135
Neurodata Without Borders (), a data standard and software ecosystem for neurophysiology, won a 2019 R&D100 award! Congrats to Oliver and the team and thanks to
@KavliFoundation
, LBL,
@HHMIJanelia
, NIH,
@SCglobalbrain
and others for support.
1
16
116
'What should we be measuring if only we had a way to'? Provide your suggestions with the Allen Frontier's Group to help direct up to $10 million in research funding.
13
61
115
Some data for reporter mouse expressing GtACR1 for supersensitive neuronal silencing ( ).
3
41
102
Exciting new conference - Neural Coding and Dynamics - in Seattle, this September!
There is space for applicants, including some of you!
Applications due May 12, 2023.
0
45
100
Finally, the jGCaMP7 preprint is out.
1/2
0
46
100
Imaging voltage in dozens of individual neurons, all in the intact brain. Spikes and subthreshold membrane fluctuations. A major step for circuit cracking.
Incredible tool from our colleagues
@ERSchreiter
@rhodamine110
and many others
@HHMIJanelia
; so many exciting avenues for future development as well.
6
59
108
0
42
84
Forgot to mention: The paper includes 40 new simultaneous recordings of spikes and calcium in transgenic mice (soon to be released). Together with the recent
@AllenInstitute
data () these data should help produce better spike inference models.
1
23
80
Amazing resource from
@Allen_Institute
. Comparison of transcriptomic cell types across V1 and ALM. GABAergic neurons are shared; glutamatergic neurons are distinct. Kudos to Bosiljka Tasic, Hongkui Zeng and others.
0
48
76
Neuropixels probes -- major step in neurophysiology. Fantastic collaboration. Shepherded over 5 years by Tim Harris. Albert Lee pushed this project from early on; James Jun, Nick Steinmetz and others moved the probes into the lab
3
31
74
Tour de Force from the MouseLIght team
@HHMIJanelia
. More than 1,000 fully reconstructed neurons. Kudos to
@JohanWinn
, Jayaram,
@MouselightTeam
and others.
1
23
69
Motor cortex cell types in motor control. Single cell RNAseq, large-scale axonal reconstructions, and cell type specific neural coding. Kudos to Mike Economo and Sarada Viswanathan.
0
36
70
It's taking a while to write this up, so here is a pre-preprint: A reporter mouse expressing GtACR1 for supersensitive neuronal silencing (). Great work by Susu Chen, Hidehiko Inagaki, Caying Guo. Construct from
@M__Mahn
@OferYizhar
0
18
69
Hard to overstate Gyuri's influence on i) electrophysiology; ii) dynamics of hippocampus. & one of the most fashionable blokes in the field!
0
22
39
1
19
63
The data provide clear evidence for the paradoxical effect, predicted > 20 years ago by Tsodyks et al: photoexcited GABAergic interneurons show a reduction in activity --> evidence for inhibition stabilized networks ;
#bioRxiv
1
21
63
Preprint describing thy-1 jRGECO1a mice from
@janeliagenie
(). Mice are available at JAX and should be useful for a wide range of imaging applications.
0
40
62
Pat Brown on why he quit his dream job and started Impossible Foods. Inspiring.
@HHMIJanelia
0
13
61
Tom Insel giving kudos to Alice Robbie’s and Kristen Branson’s (from
@HHMIJanelia
) pioneering effort to deconstruct behavior.
0
4
59
As usual, the paper scratches only the surface of this amazing data set. These simultaneous, multi-regional recordings are an exciting substrate for additional discovery. Data here: (6/7)
0
4
57
To really appreciate the data go to the MouseLight browser () and search by source or target. Feedback appreciated.
1
23
52
Thy1-jRGECO1a mice now at JAX. Wide-field ca imaging through the skull without vascular artifacts! Map of retinotopy (Ondrej Novak,
@janeliagenie
).
0
28
49
Googled the structure of Gabazine. 10 min later, this is my WAPO front page. Great achievements in computer science at Google.
5
1
46
Coding of choice and action exhibited strong correlations across brain areas. Neural dynamics changes rapidly (~ 10 ms) with the transition from choice to action, and this change in dynamics is tightly coordinated across brain regions. (5/7)
0
2
47
My buddy Bertalan Andrásfalvy below his brain-inspired mobile 'birth of an idea'. Super cool (and complex). At
@HHMIJanelia
.
3
16
43
New AAV for circuit cracking . Fantastic for all kinds of retrograde experiments. Congrats to all!
1
35
41
Perfect timing
@anne_churchland
. Our lab retreat starts tonight, with two days of prospective discussion. Topic one: Behavior in the lab. Spontaneous vs ethologically-inspired vs conditioned; etc
At request of many tweeps, here's our view: Let's not think of behavior as 1D: reductionist vs complex. Instead, consider a higher D space, and use it to evaluate tradeoffs in behavior that can inform experimental design
@analog_ashley
@erlichlab
@edyong
2
60
108
1
3
43
Neurophysiologist: consider adopting NWB:N for data sharing ,archiving etc
Neurophysiology scientists & engineers at our Institute for Brain Science hosted leading
@Kitware
developers at an inaugural hackathon event to support Neurodata Without Borders: Neurophysiology. NWB:N is a unified data format for cellular-based neurophysiology data.
#OpenScience
4
19
54
2
15
40
WaveSurfer: Open-source, free software for intracellular ephys and general lab IO. My lab uses it all the time for all sorts of things. Check out the SFN poster
and website
0
27
39
MouseLight project database. Amazing neurons & resource. With lots of fun collaborators.
0
16
37
Interested in moving your high-value neurophys. data into a standardized, widely used data format, NWB? Learn to use NWB with DataJoint? Join the NWB:N User Days, May 13-14, 2019
0
16
36
Folks, this is just too sweet. Danica Roem (VA) defeated VA's 'chief homophobe' (his term) in a race for delegate. Danica will be the first transgender person in state-wide office.
1
5
36
Happy Tim Harris and
@DiegoGutnisky
: after 4 yrs, NeuroPixel probes arrive; 960 recording sites, 10 mm shanks.
0
5
34
2-p microscope with subcellular resolution and 5 mm field of view ()! Kudos to
@sofroniewn
and Dan Flickinger.
2
45
34
Congrats Chris! But in a suit? Where's the hoodie?
Chris Harvey accepting the 2018 SfN Young Investigator Award! Extremely well deserved, and I’m so proud of him 🤗
#SfN18
2
2
23
1
1
36
@adam_k_glaser
We at the
@AllenInstitute
for Neural Dynamics are thrilled to share Exa-SPIM, a microscope and related histology methods developed to trace neurons through centimeter-scale brain specimens, including the whole mouse brain (and other applications).
1
5
35
Identifying the circuit loci showing early behavioral choice coding is foundational for neural circuit models of decision-making. Choice coding arises in a specific multi-regional circuit distributed across the brain, primarily in ALM and ALM-projection zones. (4/7)
0
2
34
@brunocolumbia
The times are very different. Right now, speaking up for evidence-based decision-making on policy is political. Science is therefore political and scientists should be political. Scientists obviously should avoid seeming unnecessarily partisan.
0
5
32
Interested in motor preparation and short-term memory? Check out our preprints &
0
12
30
Game-changing recording technology
#Neuropixels
, the new neural-recording technology that lets researchers simultaneously monitor hundreds of neurons throughout an animal's brain, is now available for researchers to purchase.
0
58
112
0
6
30
Prince's 1984 recording of Nothing Compares 2 U released for the first time (). The footage is form a rehearsal. Awesome! This is how the greats practice.
0
1
28
Nice story (and the omnipresent neurons with blue, myelinated, wiggly axons) on Mike and Sarada's paper.
0
11
28
Motor cortex cell types in motor control. Fun and fruitful collaboration with
@Allen_Institute
@realMouseLight
& Looger lab
0
17
28
We are reporting anatomy-guided recordings in multi-regional circuits, with up to 5 Neuropixels probes and inactivation of motor cortex (ALM). 70,000 units after stringent quality control, all registered to the CCF with < 100 um resolution (see also Liu et al eNeuro 2021) (2/7).
0
1
29
@bsauerbrei1
@eLife
I presume this is a rhetorical question. Some of the best papers of the last decade are in eLife. If your institution does not accept eLife papers (or any other journal or archive for that matter) for promotion run!
1
2
27
Nice characterization of soma-localized, anion-selective channelrhodopsins. Avoid 'complex activity in the axonal compartment'. This approach has worked for us as well.
1
13
26
Negative image in L4 INs suppresses self-movement signals in somatosens.
. Congrats to Jianing Yu &
@DiegoGutnisky
.
2
15
25
Limits on light power for 2p u-scopy in mice. Basic measurement for in vivo imaging, long overdue.
1
37
25
Movies illustrating some use-cases of the new large FOV microscope (2p-RAM)
1
28
25
Theorists:
1.) Vast majority of cortical spikes accounted for in terms of behavior.
2.) Low-noise encoding of tactile features in cortex.
Our full dataset of L4 S1 during behavior (Hires et al 2015) online @ CRCNS!
@svoboda314
@jianing1962
@DiegoGutnisky
0
4
19
0
15
26
Recent example of 'optotagging':
BUT this method is artisanal ... one cell type at a time. LOTs of issues with voltage imaging as well. In my opinion a method relying on electrons, without photons in between, will eventually win out.
@schoppik
@SteinmetzNeuro
@eboyden3
@svoboda314
@rhodamine110
@Abdelfattah__A
@ERSchreiter
@MishaAhrens
@AdamEzraCohen
@YoavAdam
Ooo, not sure I know about those - can you shoot me a link to an example ?
1
0
0
2
5
25
Collaborate with outstanding experimentalists, engineers and data scientists to understand how brain-wide neural circuits perform the computations underlying flexible behavior ().
2/2
2
2
22
We are eager to distribute the 2p-RAM technology. If you are interested, get in touch.
0
17
21
@CT_Bergstrom
What UIUC is doing is audacious and inspiring. Exactly what a STEM-heavy university should be doing to help figure this thing out for all of us. It's not just the massive testing, but contact tracing, dedicated dorms for quarantine ('covid colonies').
1
1
22
@buccino_alessio
@AllenInstitute
First preprint from
@AllenInstitute
for Neural Dynamics - focused on compression of
#ephys
data and its impact on spike sorting! Congrats to
@buccino_alessio
,
@OlivierWinter
, David Bryant,
@dyfbrain
& Josh Siegle!
0
1
22
Jeremy Freeman
@thefreemanlab
talking about Chan Zuckerberg science initiatives - data sharing is key
0
1
21
badass stuff from
@dddavi
Whole brain of an adult Drosophila, EM-imaged at synaptic resolution:
6
186
292
0
7
21
For a data tutorial organized in jupyter notebooks (thanks to Thinh Nguyen
@datajoint
):
. If you are interested, get in touch. (7/7)
0
0
22
Lovely collaborative paper, from
@MikeEconomo
, Sarada Viswanathan,
@realMouseLight
, and
@AllenInstitute
. Analysis of cortical output neurons based on a confluence of transcriptomics, neuronal structure, and neural coding.
A team of scientists from Janelia and
@alleninstitute
combined genetic analyses, anatomical maps, and detailed studies of neuronal activity to reveal brain cells’ complementary roles in controlling movement.
0
27
49
0
6
20
Delighted and humbled by the kudos. The work you note involved key contributors Nuo Li (Baylor), Zengcai Guo (Tsinghua), Hidehiko Inagaki (Max Planck Fl),
@ShaulDr
(Stanford),
@ratecoding
, Kayvon Daie, &
@MikeEconomo
(now BU) and others.
#collaboration
@AleksBadura
@BirdNeuro
Aww! I am humbled by your nomination, Aleksandra!
I personally believe recent works by
@svoboda314
, on the preparatory activity (via thalamo-cortico-cerebellar loops), and chasing down the attractor dynamics hypothesis is an excellent example of rigorous & game-changing science.
0
0
5
0
1
20
Today AM: Check out Kayvon's SFN poster on sculpting neural activity trajectories during motor planning. Implications for models of short-term memory.
#sfn2018
0
1
20
The MAP data set includes recordings from ALM and regions downstream of ALM, as well as regions downstream of those regions, distributed over the forebrain, midbrain and hindbrain.
0
1
21
No photons!
Less cryptically: A method that probes the cell type-specific extracellular field using high-density electrodes. E.g. something like this:
Long way to go but promising and this would scale.
@svoboda314
To be ornery and pedantic, there are always photons in between. But agreed, it’d be great if we didn’t need fluorescence.
0
0
0
1
5
18
Exa-SPIM development was led by
@AllenInstitute
for Neural Dynamics scientists
@adam_k_glaser
and
@vcj029
, with contributions from
@dyfbrain
,
@poofjunior
, Naveen Ouellette, Judith Baka, and others, as well as friends at
@cziscienceand
the
@AllenInstitute
for Brain Science.
0
5
19
2019 biomass. Cows outweigh all remaining wild vertebrates by 10x
2
4
18
What, transcriptomic clusters is not all there is to cell types and circuits🙃?
0
4
18
Kevin is a great choice for helping to lead the Kavli
In this Q&A, our new VP of Science Programs, Kevin Moses, Ph.D., talks about making the jump to science philanthropy from academia, and the challenge of funding breakthrough science:
@HHMIJanelia
@wellcometrust
@cziscience
0
2
7
0
0
17
2/4 The answer is no. We report multiple discrepancies (some obvious, others not) when performing standard population analyses on the two types of data, which were not easily resolved by commonly used spike inference algorithms applied to the fluorescence data.
1
2
17
A genius, a scientific giant and a mensh. RIP Roger.
0
14
17
Congrats
@emily_liman
! This is a big deal.
Excited to report today the molecular identity of the proton channel in sour taste cells. It is otopetrin1 - found in vestibular system, gut, fat cells, but function was not known. Conserved from humans to nematodes. Shows power of basic science!
5
94
216
0
7
17
Ascending signals from the midbrain pedunculopontine / midbrain reticular nuclei ascent via the thalamus to motor cortex. These signals are necessary and sufficient to trigger the state switch in cortex and transition behavior from planning to movement. 4/4
1
0
16
Lots of advances in voltage imaging, especially on the probes front.
#SfN2018
check out Wed AM for an update from
@janeliagenie
@HHMIJanelia
:
0
5
15
Unique opportunity to start a new research area at Janelia. Think different.
Do you have the next big idea in the life sciences? HHMI is looking for the next research area for Janelia and a scientist to lead it.
0
107
126
0
4
15
@HHMIJanelia
@nature
@ratecoding
Really enjoyable project, driven forward by Hidehiko Inagaki and
@lorifonto
. Also, super-useful reviewer reports that made the paper better; Tx!
0
0
14
@MillerLabMIT
@jmourabarbosa
@synapticlee
@ratecoding
Motor preparation and WM both are short-term memories relying on internally maintained neural dynamics. Both store information for later use (movement execution vs computation). I would be very surprised if they don't share mechanisms. We'll know soon.
2
0
14
Congrats to our colleague and friend Martha Zlatic for the Kandel / Hertie / FENS Young Investigator Prize!
0
6
14
Never seen a scarier graph
Yeah, this isn't normal.
Follow
@ZLabe
@Weather_West
@Climatologist49
for more.
Folks, we're in a climate emergency. Tell everyone you know.
67
2K
981
1
25
14
3/4 We developed a phenomenological model linking spiking and fluorescence, based on simultaneously recorded spikes and fluorescence from individual neurons. Individual neurons have different model parameters, which produces challenges for spike inference.
0
3
14
The amazing Amy Bastian giving a public talk at old ox brewery
1
0
13
@neurowitz
Whoa ... it's nice to deam, but you are off by many orders of magnitude in photon budget.
0
1
13
Sensitive red protein indicators and their characterization in flies, worms, mice etc
0
11
12
4/4 Synthetic-imaging data based on the model and recorded spikes recapitulates the discrepancies between ephys and calcium imaging. This approach can be used to understand possible confounds in imaging data.
1
2
13
- based on publicly available data from Peron et al 2015. A feather in our cap, and incentive to share data!
0
9
13
The new red GECIs (jRGECOa, jRCaMP1a,b): big step forward, but more work to do for imaging the mouse brain in vivo
0
10
12
tiago goncalves (salk) highlights jrgeco1a from
@janeliagenie
for deep tissue cellular imaging (in the dentate gyrus)
2
5
11
Republicans are making porn great again! xHamster reports a 184% increase in traffic from Cleveland.
1
12
12