"Learning produces a hippocampal cognitive map in the form of an orthogonalized state machine" by Sun et al. 2023 (Nelston Spruston lab at #HHMIJanelia) https://www.biorxiv.org/content/10.1101/2023.08.03.551900v2

"We show that a Hidden Markov Model (HMM) and a biologically plausible recurrent neural network trained using Hebbian learning can both capture core aspects of the learning dynamics and the orthogonalized representational structure in neural activity. In contrast, we show that gradient-based learning of sequence models such as Long Short-Term Memory networks (LSTMs) and Transformers do not naturally produce such representations."

#neuroscience

@flypapers

Dissecting neural circuits for cold nociception in the #Drosophila larva, by Atit Patel in D. Cox lab: http://biorxiv.org/content/10.1101/2023.07.31.551339v1

Atit was a visitor of my former lab at #HHMIJanelia. Took years to map the circuit, identify GAL4 lines, design and run behavioral assays and make sense of it all. Atit, a PhD student, did all the mapping and all the experiments and wrote most of the paper, and did a great job at it.

For the insiders: this is about class III md (multidendritic) somatosensory neurons in the fly larva, and their synaptic connectivity, primarily onto various Basin neurons (Ohyama, Schneider-Mizell et al. 2015 https://www.nature.com/articles/nature14297 , Jovanic, Schneider-Mizell et al. et al. 2016 https://www.sciencedirect.com/science/article/pii/S0092867416312429 ) but also other neurons such as Down-and-Back (Burgos et al. 2018 https://elifesciences.org/articles/26016 ) and PNs of the class IV mds (Gerhard et al. 2017 https://elifesciences.org/articles/29089 ).

In other words, how somatosensoty neurons for cold nociception (class III mds) feed into the local circuits that process nociception (class IV mds) and mechanoreception (chordotonals).

Note this work is unrelated to how the larva senses and responds to cold and warm stimuli (Hernandez-Nunez et al. 2021 https://www.science.org/doi/abs/10.1126/sciadv.abg6707 )

#neuroscience #nociception #connectomics

The #HHMIJanelia FlyEM MANC #connectome is now available on NeuronBridge.janelia.org. #Drosophila #Neuroscience researchers can use this tool to match the MANC electron #microscopy (EM) data against light microscopy (LM) data, like that from the Janelia FlyLight project. A user can interactively examine matches right in the browser by clicking the "View in 3D" button. Interactive views are sharable, too... (1/3)

Don't miss this opening for a web developer in scientific computing at #HHMIJanelia (#FediHire, #FediHired): https://hhmi.wd1.myworkdayjobs.com/en-US/External/job/Senior-Software-Engineer---Web-Applications_R-2142. Help us grow our list of innovative #OpenScience (#foss) projects: https://github.com/JaneliaSciComp/awesome-janelia-software. Janelia welcomes and values diversity, and encourages applications from people of all backgrounds, including people of color and members of groups traditionally underrepresented in science.

"Systematic annotation of a complete adult male Drosophila nerve cord connectome reveals principles of functional organisation", by Marin et al. 2023 (Greg Jefferis lab at #MRCLMB in collaboration with #HHMIJanelia and others).

https://www.biorxiv.org/content/10.1101/2023.06.05.543407v1

On the analysis of the #Drosophila male adult nerve cord (#MANC), reconstructed from #VolumeEM by Takemura et al. 2023 (preprint still pending to come out).

#neuroscience #connectomics

Takashi Kawase has released a #linux version of VVDViewer (https://github.com/JaneliaSciComp/VVDViewer), a powerful volume renderer (#scivis, #sciviz) for #fluorescence #microscopy data. To celebrate, here is a video rendered by VVDViewer as driven by the Linux version of neuVid. The input to neuVid is a high-level description of the video, in this case showing four #drosophila lines from the #HHMIJanelia FlyLight Gen1 MCFO collection. The input text is pretty simple... (1/3)

Today's #neuroscience news includes the release of the first fully-reconstructed #connectome for the ventral nerve cord (VNC) of the adult #drosophila. This data set, known as the "MANC", is the result of collaboration between the FlyEM team at #HHMIJanelia and teams from the University of #Cambridge and #Google Research. (1/5)

https://www.youtube.com/watch?v=0sKpSVZacyA

Experimental instrumentation doesn't have to be expensive: Frank Loesche @fra_loe in the Reiser lab at #HHMIJanelia build "a complete ~$300 system, including a cold-anesthesia tethering stage, that is ideal for hands-on teaching laboratories." And released all the CAD files and software as open source. How cool is that:

"We replaced expensive optomechanical and custom machined components with off-the-shelf and 3D-printed parts, and built the system around a low-cost camera that achieves 180 Hz imaging and an inexpensive tablet computer to present view-angle-corrected stimuli updated through a local network."

https://www.frontiersin.org/articles/10.3389/fnbeh.2021.689573/full

Could easily be put to good use to modernize hands-on labs at the undergrad level, perhaps also at the senior high school level.

#Drosophila #neuroscience #EducationalMaterials

Junior Scientist Workshop on Theoretical Biophysics at #HHMIJanelia

October 1-6, 2023

Apply by June 21st at https://janelia.org/you-janelia/conferences/junior-scientist-workshop-on-theoretical-biophysics

Hotel, food and travel expenses all covered.

Organised by Ann Hermunstad, James Fitzgerald and Allyson Sgro.

#science #academia #biophysics #workshop #neuroscience

There are two openings in the Mechanistic Cognitive Neuroscience NeuroEngineering Team at #HHMIJanelia, for an electromechanical engineer and an optical engineer. Come develop new #engineering tools for #Neuroscience research. Janelia welcomes and values diversity, and encourages applications from people of all backgrounds, including people of color and members of groups traditionally underrepresented in science. (#FediHire, #FediHired)

https://hhmi.wd1.myworkdayjobs.com/en-US/External/job/Janelia-Research-Campus/Electromechanical-Engineer--MCN-NET_R-1996

https://hhmi.wd1.myworkdayjobs.com/en-US/External/job/Janelia-Research-Campus/Optical-Engineer--MCN-NET_R-1995

The Scientific Computing group at #HHMIJanelia seeks a software engineer, to work on large-scale electron #microscopy reconstruction and analysis. Come work at the forefront of #imaging and #OpenScience with applications in #Neuroscience and #CellBiology. Janelia welcomes and values diversity, and encourages applications from people of all backgrounds, including people of color and members of groups traditionally underrepresented in science. (#FediHire, #FediHired)

https://hhmi.wd1.myworkdayjobs.com/en-US/External/job/Scientific-Computing-Software-Engineer_R-1972

Imaging experts: #HHMIJanelia is hiring:

https://www.janelia.org/careers/scientific-imaging-careers-available-at-janelia

Openings in imaging, instrumentation development, sample preparation & biology, and image analysis & software development.

#academia #ScienceJobs #jobs

HHMI is raising the entry-level postdoc salary to $70,000.

See the new salary scales: https://hhmi.org/sites/default/files/hhmi-postdoctoral-associate-scale.pdf

I hope the UK takes note. Presently it's about 50% of that figure, despite costs of living being about the same, particularly child care and housing.

But HHMI goes beyond that: there's flexibility to bring in entry-level postdocs at $91,000 when under heavy competition from industry (i.e., computer scientists).

#HHMIJanelia has had this flexibility–using fancy alternative job descriptions–since at least 2012 and likely earlier. I know first hand, from having run a lab there.

#HHMI #postdoc #academia #UK #USA

https://www.hhmi.org/news/hhmi-announces-postdoc-salary-changes

Spread the word to grad students and postdocs: we are hosting a junior scientist workshop on theoretical biophysics at #HHMIJanelia! Applications due 6/21: https://www.janelia.org/you-janelia/conferences/junior-scientist-workshop-on-theoretical-biophysics

Harald Hess awarded the 2023 James Prize in Science and Technology Integration by the US National Academy of Sciences: https://www.nasonline.org/programs/awards/2023-awards/Hess.html

At #HHMIJanelia, the lab of Harald Hess revolutionized electron microscopy with enhanced FIBSEM (C. Shan Xu et al. 2017 @eLife https://elifesciences.org/articles/25916 ) –now in use by us at #MRCLMB, and applied for whole #Drosophila CNS imaging; built an automated STEM to image the whole #Drosophila larval body at 5x5x35 nm; and so much more. Hats off! Congratulations!

VVDViewer is a powerful, interactive volume renderer (#scivis, #sciviz) for #fluorescence #microscopy data, developed by Takashi Kawase and Hideo Otsuna at #HHMIJanelia. The source code and built executables are available at https://github.com/takashi310/VVD_Viewer. (1/4)

Today is the last day to apply to the neuro-evo conference at #HHMIJanelia!

Apply here: https://www.janelia.org/you-janelia/conferences/neuro-evo-a-comparative-approach-to-cracking-circuit-function-iii

Dates: May 15-18, 2023.

#NeuroEvo #Janelia #HHMI #conference #neuroscience #connectomics #DevBio #EvoDevo

https://mathstodon.xyz/@albertcardona/109405695524270512

Happy birthday to the "hemibrain", a #Drosophila #neuroscience data set released by #HHMIJanelia on January 22, 2020. At that time it was the largest synaptic-level #connectome ever reconstructed, the result of years of hard work by the FlyEM team, led by Steve Plaza, and collaborators at Google. (1/3)

https://www.youtube.com/watch?v=PeyHKdmBpqY

@lili it looks like there are now at least a couple of positions in #HHMIJanelia labs for remote software consultants, if that is still of interest.

https://www.janelia.org/node/67979

Interested in #OpenScience and open software (#foss)? There are multiple openings at #HHMIJanelia:

https://www.janelia.org/node/67979

There are openings for software engineers and postdocs, in the Scientific Computing group and several Computation and Theory labs. Remote positions as contractors are possible.

Janelia welcomes and values diversity, and encourages applications from people of all backgrounds, including people of color and members of groups traditionally underrepresented in science.