Austin E. Y. T. Lefebvre

Do you LOVE organelles?? Well I am THRILLED to announce that Nellie has been published in @naturemethods! Nellie a fully automated pipeline for organelle segmentation, tracking, and hierarchical feature extraction in 2D, 3D, timelapse, multichannel live-cell microscopy 🧵1/N

We’re excited to announce FDA Orphan Drug Designation for ABBV-CLS-628, an investigational therapy to treat ADPKD, the most common inherited kidney disease. Last month, it received Fast Track Designation and is now in a Phase 2 clinical trial. calicolabs.com/press/calico-l…

An iPSC-derived heart muscle cell assembling sarcomeres videoed through a spinning disk confocal microscope by Burnette Lab graduate student, @EmmaKoory. Alpha-actinin-2 is shown. Colors denote Z slices (red-bottom; green-middle; blue-top). Movie length- 40 hours.

An iPSC heart muscle cell forming sarcomeres videoed through a microscope by @EmmaKoory for 20 h before it dies most dramatically. This was our first try on a new microscope, and Emma now has the imaging parameters dialed in so her cells do not go POP! #CellBiology

@astormic Crazy enough, there is not... I need to add that in there. If you go to the output directory and open up the organelle csv, though, you'll see a column for t, and the number of rows for a specific t is the number of mitochondria at that timepoint.

@astormic I built both Mitometer and Nellie and I’m happy to help out if you have any troubles 😁

Mitochondrial pearling isn’t random—it’s physics. Researchers identified two mechanisms: Internal pressure from ionic flux External pulling via motors Both cause membrane tension to exceed bending energy—a Rayleigh-Plateau instability. Full paper: biorxiv.org/content/10.110…

@zck Scott Holloway fanclub

(Inspired by bumping into 3 friends (!!) on my jog tonight. Apologies for the Westlake High School physics t shirt)

One thing I increasingly appreciate is the pleasure of bumping into friends on the street. This is downstream of clean, safe streets and often in walkable, midsize cities (or neighborhoods) - hard to recreate in a car culture or a city where people have no-go zones

@sato_sato5813 Likely because the label reassignment has not been run / completed yet. If you open the "process" tab and click "Run voxel reassignment", the "Open reassigned labels image" should be clickable when it completes.

I’m hiring for a microscopy image analysis role at Calico! calicolabs.com/careers/?gh_ji… We’re looking for someone at ~recent PhD lvl who has previous experience with biological samples and analyzing microscopy datasets. Feel free to reach out with any questions!

Even mis-segregations are aesthetically pleasing

Analyzing organelles is HARD. They're complex, but critical to understanding biology. Current tools are manual, organelle-specific, or can't handle large 3D datasets. With an easy install and a click of a button, Nellie solves ALL these problems! nature.com/articles/s4159… 🧵2/N

In the physical world, almost all information is transmitted through traveling waves -- why should it be any different in your neural network? Super excited to share recent work with the brilliant @mozesjacobs: "Traveling Waves Integrate Spatial Information Through Time" 1/14

Already some cool applications for Nellie: If you're used to MitoGraph data and want some of the same outputs from Nellie, check out Gav's Python code.

New from Lefebvre and colleagues! Nellie is a comprehensive automated pipeline for studying the structure and intracellular dynamics of diverse organelles that offers accurate segmentation, tracking and feature extraction on both 2D and 3D data. nature.com/articles/s4159…

@naturemethods Thanks for the post! Hope everyone finds it useful. And don’t hesitate to reach out if you have any questions or issues!

@EmmaKoory @naturemethods Super happy to hear!!

@Austin_Lefebvre @naturemethods We love Nellie! It segments the mess that is iPSC cardiomyocyte mitochondria ~beautifully~

Do you LOVE organelles?? Well I am THRILLED to announce that Nellie has been published in @naturemethods! Nellie a fully automated pipeline for organelle segmentation, tracking, and hierarchical feature extraction in 2D, 3D, timelapse, multichannel live-cell microscopy 🧵1/N

@NoMorelSupport @naturemethods I think it could! I'm less familiar with these systems, but in general this pipeline should work on diverse datasets.

@Austin_Lefebvre @naturemethods Fantastic work on #Nellie! Quick question—can your pipeline be extended to multicellular systems, like tracking trafficking across cells in a fungal colony? Would love to hear your thoughts!

@cohenlaboratory @naturemethods Thank you Sarah!

@Austin_Lefebvre @naturemethods Congratulations, Austin! 🥳

@pablo_jack @naturemethods Yes! I've actually used this on some neuronal structures myself. Try it out and let me know!

@Austin_Lefebvre @naturemethods This is great. Can resolved segmentation in neuron with small soma or structure like axon and dentrites?