Kedar Narayan
@KedarNarayan2
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Making volume electron microscopy (volumeEM/vEM) a thing! @FredNatLab @theNCI Thoughts here are my own, I think. #VolumeEM #CLEM #FIBSEM
Joined April 2021
…and it’s out! On the cover at @CellSystemsCP Those are real #mitochondria 3D models from MitoNet predictions, emerging from the ocean of grayscale EM data - inspired by insect trays in entomology 😀 #volumeEM #DeepLearning #electronmicroscopy
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They're flanked from L to R by the 3 judges Miriam Lucas, @BogovicJohn @SasLippens and of course @EM_STP and @PaulVerkade.
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Here are the Winners of the #volumeEM @GordonConf poster competition - Stephanie Nowotarski, Ana Correia, Oda Schiotz, Nedal Darif, Connon Thomas @VolumeEM1 Congrats!
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Oh my god what a fantastic #volumeEM @GordonConf, led by @PaulVerkade and @EM_STP. A special shout out to Kara Fulton (L, Harvard) and Odara Medagerada (R, Cambridge), who have been elected as the inaugural volume EM GRS 2025 chairs!
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This is SO cool. 🏆 for good old fashioned observational science with cutting-edge #volumeEM techniques - there's still so much to learn just by looking!.
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What a fun #metadata workshop to attend, thanks Matthew Hartley! @BioimageA @EMDB_EMPIAR @AI4LifeTeam Creating #AI metadata, tools and docs for #volumeEM that are 👉USABLE BY "NON 1%er" LABS👈 is critical for compute resource and expertise limited researchers!.
And now a piece of news about it, thank you Teresa Zulueta-Coarasa and Matthew Hartley for writing it!.
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And finally, use the empanada #napari plugin to automatically segment 1000s of mitos using MitoNet (point-and-click clean up predictions as needed) - biologists, read about and download it at Give it a whirl!
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MitoNet can be used as-is for mitochondria, but you can also fine-tune the models to better fit your own unique EM data. See this thread:
empanada v2.0 is out! Default MitoNet predictions not quite doing it? (L) Now you can finetune your model! 16 patches (256x256) labeled in ~30 min; 100 iterations (8 min) later - voila! (R). More mitos (circles), better split/merge (arrows), still accurate (arrowheads) #volumeEM
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This is how MitoNet was created; image datasets and benchmarks for #DeepLearning model training are all on #EMPIAR - developers, please use these resources for #imageanalysis on #volumeEM and #electronmicroscopy data! CEM1.5M, CEM-MitoLab, MitoNet benchmarks
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OK, back to this hellscape after a bit of a gap. it's either my love for #ScienceTwitter and my #volumeEM family, or some announcement coming up 😅 Or both!.
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So happy to participate with @EM_STP @SchwabYannick @PaulVerkade @JojoBischof! Check out this excellent #volumeEM poster:
Check out the e-booklet for #volumeEM and volume #CLEM with many contributions from the community in collaboration with @zeiss_micro. Including a panel discussion with @EuroBioImaging's @JojoBischof and many great imaging scientists! .
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Find the new module here on empanada-napari plugin (L) and see best practices here: and tutorial here Obligatory eye candy (R) 😅 #bioimageanalysis #electronmicroscopy #DeepLearning
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empanada v2.0 is out! Default MitoNet predictions not quite doing it? (L) Now you can finetune your model! 16 patches (256x256) labeled in ~30 min; 100 iterations (8 min) later - voila! (R). More mitos (circles), better split/merge (arrows), still accurate (arrowheads) #volumeEM
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Folks in the #volumeEM community - here's a chance to get a citation/pat-on-the-back if you've used Zarr or other NGFFs for your image data. Ping @BogovicJohn, @normanrz & @notjustmoore!.
🚨 @BogovicJohn, @normanrz & @notjustmoore are looking for citable papers where #Zarr has been used across all fields of research. Please share references below or on the @gitchat thread:.
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A European mini-invasion at #MM2022Portland! 😅 Flying the #volumeEM flag high were @anna_steyer @PaulVerkade @EJokitalo Matthew Hartley from @emblebi (Missed you @EM__Ian) Great science and a fun time, excited to build on this!
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@EM_STP @VolumeEM1 In case you didn't recognize from the hair, that's the man himself, Boris Johnson. Source:
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SO much fun to be part of the #volumeEM community at this time - it's a weird/exciting feeling to have a ring side seat, knowing you're watching a field go through an inflection point in real time. , right @VolumeEM1?.
Shout out to the awesome author panel @cppape @PaulVerkade @avweigel @kdmicheva @Stanford_MCP @hhmijanelia @LabParton @SchwabYannick @christelgenoud @btitze @EM_STP @TheCrick @KedarNarayan2.
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