Here's a #MicroscopyMonday segmentation of some neurons from the optic lobe, or visual processing area of the #Drosophila fruit fly's brain. The #connectome for the full optic lobe was released in 2024 by #HHMIJanelia, Google, and the University of Cambridge, with support from the Wellcome Trust.
#HHMIJanelia
This segmentation of #MicroscopyMonday data reconstructs neurons of the "MANC", or male adult nerve cord, from the #Drosophila fruit fly. The nerve cord is like a spinal cord and connects the brain and muscles. #HHMIJanelia, Google, and the University of Cambridge released this work in 2023.
The #HHMIJanelia FlyEM team's project page for the hemibrain:
https://www.janelia.org/project-team/flyem/hemibrain
The neuVid system, used for creating the video:
https://github.com/connectome-neuprint/neuVid
On this day 5 years ago #HHMIJanelia and Google released the "hemibrain", a map of neural connections in much of the #Drosophila fly brain. At the time it was the largest such #connectome ever created. Here's a video from the release (polished a bit), showing the interesting shapes of the neurons.
...then proofreaders from #HHMIJanelia made fixes. Here's a tool proofreaders used, to cleave false merges by designating seeds on different neurons, which Stuart Berg's graph algorithm then separated. The video's from 5 years ago so it looks a bit old fashioned, but the tool still works!
A use of #MicroscopyMonday data is making segmentations. Here's one, of #Drosophila protocerebral bridge and nodulus neurons, from the 2020 Hemibrain by #HHMIJanelia and Google. Michał Januszewski and Viren Jain's team made an initial segmentation with #AI flood-fill algorithms...
On this day 5 years ago, I released version 1.0 of neuVid. It takes high-level descriptions of #Neuroscience or #CellBiology videos and renders them with #Blender or VVD Viewer. Here's a montage of how I've used it. Thanks to #HHMIJanelia for support, especially Steve Plaza and Stuart Berg of FlyEM.
The #HHMIJanelia FlyEM team's optic lobe page:
https://www.janelia.org/project-team/flyem/optic-lobe
Documentation for neuVid:
https://github.com/connectome-neuprint/neuVid
March 30 - April 2, 2025, at #HHMIJanelia: #AI Revolution Meets 4D Cellular #Physiology
"This meeting will gather current and future leaders in cellular physiology and AI for a deep discussion at this inflection point of both fields. What problems are ripe for this emerging intersection of AI and cellular physiology? Where are the challenges?"
Onsite participation application deadline: November 5, 2024
https://www.janelia.org/you-janelia/conferences/ai-revolution-meets-4d-cellular-physiology
In videos showing large sets of reconstructed neurons, revealing the neurons one after another in staggered form allows a nice glimpse of the diversity of morphologies. But staggering in what order? Here are some possibilities, for a set of 1640 cell types from the #Drosophila visual system, chosen by Shin-ya Takemura from #HHMIJanelia. First, ordering from smallest to largest, measured as bounding-box volume:
(1/4)
For #SciArtSeptember: 50 EPG neurons from the #Drosophila, segmented from electron microscopy images, rendered in #Blender3d driven by neuVid. This ring of neurons forms part of the fly’s internal compass. As the fly changes its heading, neuronal activity moves around the ring, as shown by the false color gradient. Imaging and reconstruction by #HHMIJanelia and Google Research (www.janelia.org/project-team/flyem/hemibrain); function described by Hulse et al (doi.org/10.7554/eLife.66039).
Andreas Schoofs and Anton Miroschnikow in Michael Pankratz' lab have done an astonishing amount of work manually mapping the peripheral nervous system of the larval #Drosophila, with #CATMAID, in the STEM volume we imaged and they named "Igor". Congrats on seeing this gargantuan project through!
The whole larval volume of "Igor", including all tissues, is available here, courtesy of the #OpenOrganelle project led by Aubrey Weigel @avweigel at #HHMIJanelia:
https://openorganelle.janelia.org/datasets/jrc_fly-larva-1
See it at 5x5x35 nm resolution in #neuroglancer: https://neuroglancer-demo.appspot.com/#!%7B%22dimensions%22:%7B%22x%22:%5B1e-9%2C%22m%22%5D%2C%22y%22:%5B1e-9%2C%22m%22%5D%2C%22z%22:%5B1e-9%2C%22m%22%5D%7D%2C%22position%22:%5B249600.5%2C79040.5%2C84280.5%5D%2C%22crossSectionOrientation%22:%5B0%2C1%2C0%2C0%5D%2C%22crossSectionScale%22:50%2C%22projectionOrientation%22:%5B0%2C1%2C0%2C0%5D%2C%22projectionScale%22:65536%2C%22layers%22:%5B%7B%22type%22:%22image%22%2C%22source%22:%22n5://s3://janelia-cosem-datasets/jrc_fly-larva-1/jrc_fly-larva-1.n5/em/tem-uint8%22%2C%22tab%22:%22rendering%22%2C%22opacity%22:1%2C%22blend%22:%22additive%22%2C%22shader%22:%22#uicontrol%20invlerp%20normalized%28range=%5B0%2C%20255%5D%2C%20window=%5B0%2C%20255%5D%29%5Cn#uicontrol%20vec3%20color%20color%28default=%5C%22white%5C%22%29%5Cnvoid%20main%28%29%7BemitRGB%28color%20%2A%20normalized%28%29%29%3B%7D%22%2C%22name%22:%22tem-uint8%22%7D%5D%2C%22selectedLayer%22:%7B%22visible%22:true%2C%22layer%22:%22tem-uint8%22%7D%2C%22crossSectionBackgroundColor%22:%22#000000%22%2C%22layout%22:%224panel%22%7D (control-minus and control-plus to zoom; mouse click to pan, scroll wheel to browse in Z).
Will appear at the #VirtualFlyBrain website soon as well.
There are many more peripheral nervous system components mapped, yet to be published.
This paper is open access:
"Serotonergic modulation of swallowing in a complete fly vagus nerve connectome", Schoofs et al. 2024 https://www.cell.com/current-biology/fulltext/S0960-9822(24)01137-0?rss=yes&utm_source=dlvr.it&utm_medium=mastodon
The CellMap team at #HHMIJanelia has released a new high-resolution dataset for the tissue microarchitecture of a postnatal day 7 (P7) mouse. Read the details in what @avweigel calls a "cheeky news post": https://openorganelle.janelia.org/news/2024-09-09-data-release-high-resolution-imaging-of-p7-mouse-tissue-microarchitecture
Neuroscientist Nelson Spruston named new executive director of #HHMIJanelia, replacing cell biologist Ron Vale.
#HHMI president's words are as transparent as it gets:
"Erin O’Shea, President of HHMI, said, “Nelson is the right leader at the right time in this next chapter for Janelia. With his deep knowledge about what makes the Janelia model conducive to doing great science, he can help guide Janelia both strategically and operationally to pursue important questions in the life sciences.”"
https://www.janelia.org/news/janelia-names-nelson-spruston-its-third-executive-director
Allison Truhlar just released a beautiful website describing projects from the #OpenScience Software Initiative at #HHMIJanelia: https://ossi.janelia.org
@tmalsburg At #HHMIJanelia, we recognize this. We have professional software developers in our labs, project teams, and facilities. We support junior and senior scientists to publish and maintain their software as open source, and to go the extra mile to make them user friendly with propper installers and docs. E.g. https://janeliascicomp.github.io/ossi-website/projects/
Junior Scientist Workshop on Theoretical Neuroscience at #HHMIJanelia
November 17 - 22, 2024
Last summer, #HHMIJanelia postdocs Gabriela Michel and Emmanuel Marquez Legorreta travelled to Ghana to present a course in computational #neuroscience and #machineLearning. It was so successful they are planning another course for next year, in Rwanda.
https://www.janelia.org/news/janelia-postdocs-help-organize-course-in-ghana
The latest call for imaging proposals for the Advanced Imaging Center (AIC at #HHMIJanelia) is open.
Deadline is Feb. 1, 2024.
Get to use #HHMIJanelia imaging technology and expertise for free.
Visit http://aicjanelia.org/apply to schedule a technical consultation.
#HHMIJanelia is looking for help to lead diverse annotation projects: https://hhmi.wd1.myworkdayjobs.com/en-US/External/job/Scientific-Operations-Manager--PTR-Bioimage-Annotations-and-Analysis_R-2361?locationRegionStateProvince=e0889a76c58d4fff9b54b80dadc49000
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