When #HHMIJanelia released the #Drosophila hemibrain in 2020, rendering all cell types at once with full shading/shadows was too hard, so the video showed them region by region. Technology has since advanced, and I went back and rendered them all together. I like how it shows the internal structure.

On this day 10 years ago, #Tableau released Vizable for the iPad. It gave a way to explore data with gestures: pinch/unpinch to aggregate/disaggregate, swipe to filter out, etc. The development effort, led by Robin Stewart and Dave Story, was great fun. #DataViz #DataVis

vimeo.com/142648727

Some fly neurons are “dimorphic”, existing in both males and females but connecting to different neighboring neurons. Neighbors may be “isomorphic”, the same in both male and female; or sex specific; or dimorphic themselves. Here's an example, the type AOTU012, present in left and right instances.

A connectome spanning the brain and nerve cord reveals interesting pathways. Visual-motor pathways connect visual neurons, which help the fly detect objects, to motor neurons, which help the fly move in response. Here's one such pathway, from R1-R6 visual neurons to the DNg13 motor neuron.

Come to #HHMIJanelia to work on the frontiers of AI and biology. Apply now for an AI Engineer position working on protein biosensors:

hhmi.wd1.myworkdayjobs.com/en-US/Extern...

More openings coming soon. Interesting AI is widespread at Janelia, like this diffusion model from Larissa Heinrich.

The #HHMIJanelia FuncEWorm project is building the first cellular/molecular blueprint of an entire organism, the C. elegans nematode. Here's a video showing some of what's involved: light sheet fluorescence microscopy, electron microscopy, spatial transcriptomics.

www.janelia.org/project-team...

What does a neural network look like? Maybe like this view of Larissa Heinrich's U-net for organelle segmentation, with edges between layer inputs and outputs.

Want to help build networks like this? Join #HHMIJanelia's new AI initiative as a data engineer:
hhmi.wd1.myworkdayjobs.com/en-US/Extern...

When beauty and wonder seem elusive, try HHMI's Beautiful Biology site, for a reminder of what the scientific study of nature has to offer. Noah Green and the team update the collection every week and write accessible descriptions for everything.

www.hhmi.org/beautifulbiology

We made the experimental system with a toolkit of software packages built on the #Unity3D game engine. Here's an example of a "meadow" world: on top is the fly's view warped for a panorama of four display screens, below is some simulated fly motion.

github.com/JaneliaSciCo...

I wanted a distraction from the news so I made this video, of some #Drosophila neurons with interesting morphologies: the mushroom body output neurons (MBONs). I used reconstructions from the FlyWire data set, and rendered with #Blender3D driven by 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!

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.

This #FluorescenceFriday video shows 89 volumes from the #HHMIJanelia FlyLight Split-GAL4 collection: premotor and related neurons from the #Drosophila fruit fly's equivalent of a spinal cord. I gave a high-level description of the video to neuVid, which drove rendering by VVD Viewer.

I used VVD Viewer for this #FluorescenceFriday video: 141 volumes from the #HHMIJanelia FlyLight Split-GAL4 #Drosophila driver collection. The animation comes from a high-level description processed by neuVid. Such a rapid tour of the data has questionable scientific value, but it's fun to watch!

My favorite volume renderer for fluorescence #microscopy is VVD Viewer, by Takashi Kawase and Hideo Otsuna at #HHMIJanelia. Takashi wrote fast GPU code. Hideo wrote a transfer function with 3D sampling and a final 2D power function, which together show just enough low data values for visual context.

For fun, here's one more video of #CellBiology data from the OpenOrganelle collection. This one shows nuclei and mitochondria from a sample of mouse liver tissue, made with neuVid driving #Blender.