Jacques Augenstreich
Biomedical Research Scientist - CVPath institute.
Image analysis shenanigans, mycobacterium tuberculosis, macrophages and membrane dynamics
- Reposted by Jacques Augenstreich🧬🔬🧪 🎉 Our team at @czbiohub is thrilled to share TWO companion papers out today in @NatureMethods! 📦 Ultrack — robust, scalable nD cell tracking 🌐 inTRACKtive — a beautiful, open-source web viewer for lineage exploration Let’s dive in! 👇 www.nature.com/articles/s41... www.nature.com/articles/s41...
- Reposted by Jacques Augenstreich#ZebrafishZunday: Simultaneous tracking of 100 zebrafish larvae using open-source software. Credit to FastTrack (www.fasttrack.sh). 🧪
- Reposted by Jacques Augenstreich[Not loaded yet]
- Reposted by Jacques AugenstreichWe have updated our database of funding opportunities for Early-Career Researchers (private foundations, federal, international) We have 456 entries, for which we provide $ amount, deadline, eligibility criteria, etc. Download this massive database here for free: research.jhu.edu/rdt/funding-...
- Reposted by Jacques Augenstreich[Not loaded yet]
- Reposted by Jacques AugenstreichGroundbreaking study in Cell from @leventallab.bsky.social: phospholipid asymmetry is a defining feature of the plasma membrane and cholesterol fills the holes — major implications for how this membrane works. A #lipidtime must-read! www.cell.com/cell/abstrac...
- Reposted by Jacques Augenstreich[Not loaded yet]
- Reposted by Jacques AugenstreichShout-out to @pierredupuy.bsky.social and colleagues! Excited to share our latest study, where we uncovered a previously unknown bacterial defense system in M. #tuberculosis: effluxosomes — dynamic membrane clusters that coordinate resistance to multiple toxic metals. shorturl.at/Ek0HD #MicroSky
- Reposted by Jacques Augenstreich[Not loaded yet]
- Reposted by Jacques Augenstreich[Not loaded yet]
- Reposted by Jacques Augenstreich[Not loaded yet]
- Reposted by Jacques Augenstreich[Not loaded yet]
- Reposted by Jacques Augenstreich#Cellpose 3 paper now out. Not all images are perfect. Restore your images with Cellpose3 to get better segmentations, w/ @marius10p.bsky.social www.nature.com/articles/s41...
- Reposted by Jacques Augenstreich[Not loaded yet]
- Reposted by Jacques Augenstreich[Not loaded yet]
- Reposted by Jacques Augenstreich[Not loaded yet]
- Reposted by Jacques Augenstreich[Not loaded yet]
- Reposted by Jacques Augenstreich[Not loaded yet]
- Reposted by Jacques Augenstreich[Not loaded yet]
- Reposted by Jacques AugenstreichMicroscopy Nodes is now up on bioRxiv! 🚀 This is a Blender extension that seamlessly integrates and visualizes 3D microscopy data (TIF & @zarr.dev). High-quality volume rendering for anyone, in both EM and fluorescence, regardless of computational expertise! 🔬 www.biorxiv.org/content/10.1...
- Reposted by Jacques Augenstreich[Not loaded yet]
- Reposted by Jacques AugenstreichOur fully 3D-printed microscope is featured in @newscientist.bsky.social www.newscientist.com/article/2462...
- Reposted by Jacques Augenstreich[Not loaded yet]
- The final version of our story on autophagy and time-lapse imaging is out: doi.org/10.1371/jour... (Corrected one expected on the 14th). This questioned a bit the direct role of xenophagy to digest Mtb, but show that is appearance may be useful to track phagosomal integrity in time-lapse imaging 👇
- Reposted by Jacques AugenstreichHey #StatsSky, what are you favorite papers to cite when you need to justify something that is obvious (I once had a reviewer ask we justify the use of logistic regression on a binary outcome) or when you need to push-back on silly reviewer requests (e.g., asking for p-values in table 1)?
- Reposted by Jacques Augenstreich[Not loaded yet]
- Reposted by Jacques AugenstreichNew! @jenncoughlan.bsky.social kindly shared their MIRA NIH award with our github repo. If you have a successful grant app you're willing to share, please contribute! github.com/RILAB/statem...
- Reposted by Jacques AugenstreichAnd to start 2025 strong… Our work #NanoPyx is out in Nature Methods 😍❤️ DOI: doi.org/10.1038/s415... #NanoPyx is a Python framework that uses the #LiquidEngine to efficiently accelerate bioimage analysis for any user! (1/n) ⬇️
- Reposted by Jacques AugenstreichDo you know who Douglas Prasher is? Many don't, even though he is the person who cloned the original #GFP gene in the late 1980s. In my short history of plant light #microscopy I also cover a bit of his story - & why he is relatively unknown today, despite the importance of his work. See this 🧵👇
- Reposted by Jacques AugenstreichHappy ending (of the year): the release of our preprint, "The Martini 3 Lipidome: Expanded and Refined Parameters Improve Lipid Phase Behavior", now available on @ChemRxiv. 👉 Read the full preprint here: chemrxiv.org/engage/chemr... and get the parameters here: github.com/Martini-Forc...
- Reposted by Jacques AugenstreichSon hormigas resolviendo un problema geométrico y es para flipar en colores.
- Reposted by Jacques AugenstreichHarvard and Google AI mapped one cubic millimeter of a human brain. It took up 1.4 petabytes of storage just in pictures of the specimen. So the entire brain would take ~ 1.6 zettabytes of storage, cost $50 billion, and require 140 acres. It would be the largest data center on the planet— one brain.
- Reposted by Jacques AugenstreichTaking pictures of cells with a microscope, then extracting thousands of features from them is uncannily effective for quantifying cell state, esp. for genes and chemicals (e.g., Cell Painting). But we often average the rich single-cell data to simplify analysis. Can we do better? #bioML 🧪 1/n
- Reposted by Jacques AugenstreichI finally got around to making a video about my utilities to render 3D projections in Jupyter notebooks. The code is useful but a bit rough so I also suggest taking a look at @guiwitz.bsky.social microfilm and @haesleinhuepf.bsky.social stackview as more polished options. youtu.be/9yOA8R03trE
- For people interested with a PyImageJ install also containing cellpose in the same environment, a singularity container (the file to build it) bound to 'da_tracker' is available on github now. A link to download the built container can be found as well on the main page. github.com/jaugenst/da_... 👇
- This only work on Linux. For Windows users, I'd advise to install Windows subsystem for Linux (only one command line, check here: learn.microsoft.com/en-us/window...).
- Reposted by Jacques Augenstreich[Not loaded yet]
- Reposted by Jacques Augenstreich[Not loaded yet]
- Reposted by Jacques Augenstreich[Not loaded yet]
- Reposted by Jacques AugenstreichNon-comprehensive list of projects, hardware, software, and people related to #OpenMicroscopy. List could do with some updates, so please share and suggest additions! github.com/HohlbeinLab/...
- Reposted by Jacques Augenstreich[Not loaded yet]
- Reposted by Jacques AugenstreichHappy to share my first ever (co)last author paper 🥳 reporting on how Mtb adapts its carbon diet under acid stress. A big thank you to my partners in crime @saehrt.bsky.social and @healycl.bsky.social without who this would not have been possible 😘 journals.asm.org/doi/10.1128/...
- Reposted by Jacques Augenstreich[Not loaded yet]
- A mistake can turn into an interesting time-lapse ! Here is the dynamics of Lysoview (same thing than Lysotracker) in a primary human macrophage. (1 frame every 2sec or so)
- Alright, I'll start working on it and try my best. Stay tuned !
- Reposted by Jacques AugenstreichOk, I made a starter pack for membrane trafficking and organelles (broadly defined). Feel free to self-nominate! go.bsky.app/RbtJjt7at://did:plc:qqgx2dooaid3j2qgu4d5xbxc/app.bsky.graph.starterpack/3laoqqodbfc2j
- I'm considering creating a video tutorial on bioimage analysis with PyImageJ, TrackMate, and Cellpose. It would focus on simplifying installation and include examples like multi-level tracking with single-cell and single-bacteria tracking within cells. Would anyone be interested?
- Reposted by Jacques AugenstreichMy turn to create a starter pack for scientists using live imaging in their research! Of course, I’ve likely missed many—please let me know who else I should include. Thanks! go.bsky.app/KYYr7xc #liveimaging #livevellimaging #microscopyat://did:plc:5wkrpvrno3grto7uyb6qbo5o/app.bsky.graph.starterpack/3lbenbiqtws2i
- Starting brand new on this platform, it's not to late to try our tool 'da_tracker', designed for quantitative single cell and single phagosome tracking, using PyImageJ, and Trackmate-Cellpose (So it's free): journals.biologists.com/bio/article/... Feel free to reach out if you need help to try it !
- Some updates will come to make this more accessible and user-friendly. More automated analysis will come as well, specifically for automatized quantification of protein recruitment on the bacteria. More code shenanigans can be found here: github.com/jaugenst
- Reposted by Jacques Augenstreich[Not loaded yet]
- Reposted by Jacques Augenstreich[Not loaded yet]
- Reposted by Jacques Augenstreich[Not loaded yet]
- Reposted by Jacques Augenstreich[Not loaded yet]
- Reposted by Jacques Augenstreich[Not loaded yet]
- Reposted by Jacques Augenstreich🔬 Are you eager to dive into the world of light microscopy & learn from top-notch microscopists about its essential techniques for life science applications? If that sounds exciting, don’t miss out on this free, in-depth iBiology series! 👉 www.ibiology.org/online-biolo...
- Reposted by Jacques Augenstreich[Not loaded yet]
- Reposted by Jacques Augenstreich[Not loaded yet]
