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Austin E. Y. T. Lefebvre Profile
Austin E. Y. T. Lefebvre

@Austin_Lefebvre

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Dr. Leafbeaver, DS @calico. You can't spell imaging without "im aging" and boy am I. Organelle enthusiast. Creator of Nellie and Mitometer.

San Francisco, CA
Joined September 2012
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@Austin_Lefebvre
Austin E. Y. T. Lefebvre
5 months
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
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@Austin_Lefebvre
Austin E. Y. T. Lefebvre
12 days
RT @manorlaboratory: My lab’s 5-year NIH R01 grant, awarded to study gene therapy for hearing loss, was abruptly terminated. I want to shar….
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@Austin_Lefebvre
Austin E. Y. T. Lefebvre
2 months
I’m hiring for a microscopy image analysis role at Calico!. 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!.
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@Austin_Lefebvre
Austin E. Y. T. Lefebvre
3 months
RT @loxstoplox: Even mis-segregations are aesthetically pleasing
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@Austin_Lefebvre
Austin E. Y. T. Lefebvre
4 months
RT @Austin_Lefebvre: Analyzing organelles is HARD. They're complex, but critical to understanding biology. Current tools are manual, organe….
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@Austin_Lefebvre
Austin E. Y. T. Lefebvre
4 months
RT @t_andy_keller: In the physical world, almost all information is transmitted through traveling waves -- why should it be any different i….
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@Austin_Lefebvre
Austin E. Y. T. Lefebvre
4 months
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.
@sturm_gav
Gabriel (Gav) Sturm
4 months
Nellie's image analysis capabilities are vast. I put a video of yeast mitochondria through Nellie and generated a 'live-cell MitoGraph' - a topological graph capturing mitochondrial network's fission and fusion events over time.
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@Austin_Lefebvre
Austin E. Y. T. Lefebvre
4 months
RT @naturemethods: New from Lefebvre and colleagues! Nellie is a comprehensive automated pipeline for studying the structure and intracellu….
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@Austin_Lefebvre
Austin E. Y. T. Lefebvre
5 months
Try and share Nellie today!.We've included some sample data if you want to explore what Nellie can do. Code: Paper: And please share your results with us! We're excited to see how you'll use it in your research. 🧵Fin/N.
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@Austin_Lefebvre
Austin E. Y. T. Lefebvre
5 months
We also compare Nellie to existing state of the art methods for both segmentation and tracking across imaging resolution, structure widths, and structure lengths, as well as the pipeline's speed on different sized images. 🧵14/N
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@Austin_Lefebvre
Austin E. Y. T. Lefebvre
5 months
Now we can generate flow fields and get cool metrics, like if fields are diverging from (fission?) or converging to (fusion?) a point, or whether a branch is rotating along its long axis (?? dancing?). All of this, and much much more, linked to our organellar hierarchy. 🧵13/N
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@Austin_Lefebvre
Austin E. Y. T. Lefebvre
5 months
From these beacons, we can use a distance and cost-weighted interpolation to generate tracks for any coordinate within our organelles! Even at a sub-voxel level. We can use this to link voxels (and thus objects) between temporal frames too. 🧵12/N
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@Austin_Lefebvre
Austin E. Y. T. Lefebvre
5 months
We generate internal motion capture markers (think Hollywood) and pattern match these markers between frames to create beacons that point the way for the actual tracking. This means that we don't have to rely on finicky segmentations or skeletons for tracking. 🧵11/N
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@Austin_Lefebvre
Austin E. Y. T. Lefebvre
5 months
Then Nellie breaks down the organelles into connected components, and uses its skeleton to break it down even further into branches, which break down into individual nodes, which are variable-range containers for surrounding voxels. A big hierarchical organelle tree. 🧵10/N
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@Austin_Lefebvre
Austin E. Y. T. Lefebvre
5 months
So how does Nellie actually work? First Nellie figures out your image's metadata. Then it applies an automated structural-enhancement regime (modified Frangi filter + others) to make those organelles pop. 🧵9/N
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@Austin_Lefebvre
Austin E. Y. T. Lefebvre
5 months
Before deep-diving into Nellie, shout out my co-authors: @sturm_gav, for help on all the paper, experiments, and testing, and to the other co-authors @Kayley_Hake, @bbkaufmann @emistoops, Magdalena Lopez, and Molly Lin. And of course @rita_strack for being a great editor!. 🧵8/N.
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@Austin_Lefebvre
Austin E. Y. T. Lefebvre
5 months
And just for fun, here's me walking around, masked by Meta's Segment Anything Model (@AIatMeta), and tracked via Nellie's tracking pipeline. 🧵7/N
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@Austin_Lefebvre
Austin E. Y. T. Lefebvre
5 months
We used Nellie to unmix multiple organelles from a single fluorescence channel with high accuracy using just their morphology and motility patterns with a standard (random forest) classifier. More fluorescence channels for your experiments!. 🧵6/N
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@Austin_Lefebvre
Austin E. Y. T. Lefebvre
5 months
We also analyzed the intracellular ER highways using Nellie's outputs, allowing us to understand organellar rearrangements using its topology from the perspective of graph theory. 🧵5/N
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@Austin_Lefebvre
Austin E. Y. T. Lefebvre
5 months
Inspired by @GoogleDeepMind's weather forecasting model GraphCast, we also developed an organelle graph autoencoder using Nellie's outputs to analyze mitochondrial networks' responses to ionomycin treatment, revealing complex dynamics invisible to traditional analysis. 🧵4/N
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@Austin_Lefebvre
Austin E. Y. T. Lefebvre
5 months
Nellie is FULLY automated with NO parameters to tune, and works on ALL structures - from mitochondria to ER to microtubules and beyond. (credit to @AndrewGYork and @amsikking's Snouty SOLS microscope for the data, and @AlisterBurt for the Napari Animation plugin). 🧵3/N
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