Jacques Augenstreich
@augenstreich.bsky.social
Biomedical Research Scientist - CVPath institute.
Image analysis shenanigans, mycobacterium tuberculosis, macrophages and membrane dynamics
Image analysis shenanigans, mycobacterium tuberculosis, macrophages and membrane dynamics
Pinned
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 !
Feel free to reach out if you need help to try it !
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...
📦 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...
August 25, 2025 at 9:06 AM
🧬🔬🧪 🎉 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...
📦 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). 🧪
June 15, 2025 at 8:10 AM
#ZebrafishZunday: Simultaneous tracking of 100 zebrafish larvae using open-source software. Credit to FastTrack (www.fasttrack.sh). 🧪
Reposted by Jacques Augenstreich
It is my real pleasure to share our ASAP article published in ACS Infect Dis.
Another great collaboration with @pierresantucci.bsky.social @canaanlab.bsky.social
@lkremer1.bsky.social
@ibmm-balard.bsky.social
@map-proteomique.bsky.social
and more...
Enjoy 😊
pubs.acs.org/doi/10.1021/...
Another great collaboration with @pierresantucci.bsky.social @canaanlab.bsky.social
@lkremer1.bsky.social
@ibmm-balard.bsky.social
@map-proteomique.bsky.social
and more...
Enjoy 😊
pubs.acs.org/doi/10.1021/...
Mapping of Mycobacterial Enzymes Involved in Triacylglycerol Accumulation as Intrabacterial Lipid Inclusions Using Activity-Based Multitarget Inhibitor Probes
Lipids play a critical role in the physiology, life cycle, and pathogenicity of mycobacteria. They largely participate in host–pathogen interactions and fulfill important functions ranging from cell w...
pubs.acs.org
May 29, 2025 at 1:11 PM
It is my real pleasure to share our ASAP article published in ACS Infect Dis.
Another great collaboration with @pierresantucci.bsky.social @canaanlab.bsky.social
@lkremer1.bsky.social
@ibmm-balard.bsky.social
@map-proteomique.bsky.social
and more...
Enjoy 😊
pubs.acs.org/doi/10.1021/...
Another great collaboration with @pierresantucci.bsky.social @canaanlab.bsky.social
@lkremer1.bsky.social
@ibmm-balard.bsky.social
@map-proteomique.bsky.social
and more...
Enjoy 😊
pubs.acs.org/doi/10.1021/...
Reposted by Jacques Augenstreich
We 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-...
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-...
May 7, 2025 at 4:46 PM
We 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-...
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
In this week's #mitophagy papers, Rab GTPases take the centre stage, with a systematic study their role in autophagy, showing that multiple "Rabs" selectively mediate the degradation of mitochondria and other cellular components.
Thanks to @biomednews.bsky.social
biomed.news/bims-tofagi/...
Thanks to @biomednews.bsky.social
biomed.news/bims-tofagi/...
April 13, 2025 at 11:29 AM
In this week's #mitophagy papers, Rab GTPases take the centre stage, with a systematic study their role in autophagy, showing that multiple "Rabs" selectively mediate the degradation of mitochondria and other cellular components.
Thanks to @biomednews.bsky.social
biomed.news/bims-tofagi/...
Thanks to @biomednews.bsky.social
biomed.news/bims-tofagi/...
Reposted by Jacques Augenstreich
Groundbreaking 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...
Cell membranes sustain phospholipid imbalance via cholesterol asymmetry
This work challenges a major assumption in cell biology by showing that lipid bilayers
can have drastically different phospholipid abundances between their two leaflets.
This lipid abundance asymmetry...
www.cell.com
April 3, 2025 at 3:07 PM
Groundbreaking 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
Pleased to highlight a new preprint from the lab. This is the work of my longtime collaborator in the lab Allison Fay, who wanated to create new tools for disocvery biology in mycobacteria, specifically a new sysem for protein localizaton and proximity proteomics.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
March 25, 2025 at 2:54 PM
Pleased to highlight a new preprint from the lab. This is the work of my longtime collaborator in the lab Allison Fay, who wanated to create new tools for disocvery biology in mycobacteria, specifically a new sysem for protein localizaton and proximity proteomics.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Jacques Augenstreich
Shout-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
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
March 27, 2025 at 6:09 AM
Shout-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
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
Any1 is a phospholipid scramblase involved in #endosome biogenesis, say Jieqiong Gao, Christian Ungermann and colleagues (Osnabrück University): rupress.org/jcb/article/...
#Membrane #lipid #Organelles #Biochemistry
#Membrane #lipid #Organelles #Biochemistry
March 13, 2025 at 2:38 PM
Any1 is a phospholipid scramblase involved in #endosome biogenesis, say Jieqiong Gao, Christian Ungermann and colleagues (Osnabrück University): rupress.org/jcb/article/...
#Membrane #lipid #Organelles #Biochemistry
#Membrane #lipid #Organelles #Biochemistry
Reposted by Jacques Augenstreich
Excited to share our last study. Huge congrats to Sarah Monard, Arnaud Métais, @gclugo.bsky.social, @chrisverollet.bsky.social and all colleagues!
We have found a mysterious cell type inside TB lung lesions that seems neuron-like but isn't quite a nerve cell.
Let's dive in👇
shorturl.at/x4Sb5
We have found a mysterious cell type inside TB lung lesions that seems neuron-like but isn't quite a nerve cell.
Let's dive in👇
shorturl.at/x4Sb5
March 13, 2025 at 6:43 AM
Excited to share our last study. Huge congrats to Sarah Monard, Arnaud Métais, @gclugo.bsky.social, @chrisverollet.bsky.social and all colleagues!
We have found a mysterious cell type inside TB lung lesions that seems neuron-like but isn't quite a nerve cell.
Let's dive in👇
shorturl.at/x4Sb5
We have found a mysterious cell type inside TB lung lesions that seems neuron-like but isn't quite a nerve cell.
Let's dive in👇
shorturl.at/x4Sb5
Reposted by Jacques Augenstreich
Wow, this is big: "Fiji can now be launched in a Python-first mode, where first Python is started, then Fiji is started via the PyImageJ library. In this mode, Fiji is fully integrated with the active Python environment"
forum.image.sc/t/fiji-2024-...
forum.image.sc/t/fiji-2024-...
Fiji 2024 Year in Review: Milestones and Roadmap
Introduction The Fiji team at LOCI is pleased to share significant progress on several major initiatives as we work towards raising the technological standards of Fiji. These include Fiji 2.16.0, feat...
forum.image.sc
March 1, 2025 at 12:01 PM
Wow, this is big: "Fiji can now be launched in a Python-first mode, where first Python is started, then Fiji is started via the PyImageJ library. In this mode, Fiji is fully integrated with the active Python environment"
forum.image.sc/t/fiji-2024-...
forum.image.sc/t/fiji-2024-...
Reposted by Jacques Augenstreich
Luminescent sensing of conformational integrin activation in living cells
www.cell.com/cell-reports...
www.cell.com/cell-reports...
Luminescent sensing of conformational integrin activation in living cells
Villari et al. present the generation of a luminescent reporter for a β1 integrin
activation sensor (β1IAS). A siRNA HTS on β1IAS KI endothelial cells revealed previously
uncharacterized regulators of...
www.cell.com
February 18, 2025 at 8:43 PM
Luminescent sensing of conformational integrin activation in living cells
www.cell.com/cell-reports...
www.cell.com/cell-reports...
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...
February 12, 2025 at 11:10 AM
#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
1. A thread about the value of doing "slow science": When I was in grad school I heard this (likely apocryphal) story about one of my favourite scientists: Barbara McClintock.
January 31, 2025 at 6:20 PM
1. A thread about the value of doing "slow science": When I was in grad school I heard this (likely apocryphal) story about one of my favourite scientists: Barbara McClintock.
Reposted by Jacques Augenstreich
It’s incredibly hard to study lipids in biological membranes on the nanoscale. You need near-perfect information on both membrane ultrastructure and lipid density, which usually isn’t attainable. Lipid-CLEM brought to you by @mathilda95.bsky.social changes that.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
January 31, 2025 at 10:28 AM
It’s incredibly hard to study lipids in biological membranes on the nanoscale. You need near-perfect information on both membrane ultrastructure and lipid density, which usually isn’t attainable. Lipid-CLEM brought to you by @mathilda95.bsky.social changes that.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Jacques Augenstreich
Are you planning your lectures/course content for this year? Check out MyScope – our free #microscopy training website with theory, quizzes and microscope simulators 🧪
Developed by our experts, open to the global community: www.myscope.training
#openlearning
Developed by our experts, open to the global community: www.myscope.training
#openlearning
January 30, 2025 at 5:45 AM
Are you planning your lectures/course content for this year? Check out MyScope – our free #microscopy training website with theory, quizzes and microscope simulators 🧪
Developed by our experts, open to the global community: www.myscope.training
#openlearning
Developed by our experts, open to the global community: www.myscope.training
#openlearning
Reposted by Jacques Augenstreich
Reposted by Jacques Augenstreich
Fantastic resource for bio icons: NIH Bioart Source
Build figures, presentations, and illustrations with 2,000+ science and medical art visuals. This collection of high-quality, scientifically accurate vectors, #icons, and brushes is freely available within the public domain. bioart.niaid.nih.gov
Build figures, presentations, and illustrations with 2,000+ science and medical art visuals. This collection of high-quality, scientifically accurate vectors, #icons, and brushes is freely available within the public domain. bioart.niaid.nih.gov
October 29, 2024 at 7:19 AM
Fantastic resource for bio icons: NIH Bioart Source
Build figures, presentations, and illustrations with 2,000+ science and medical art visuals. This collection of high-quality, scientifically accurate vectors, #icons, and brushes is freely available within the public domain. bioart.niaid.nih.gov
Build figures, presentations, and illustrations with 2,000+ science and medical art visuals. This collection of high-quality, scientifically accurate vectors, #icons, and brushes is freely available within the public domain. bioart.niaid.nih.gov
Reposted by Jacques Augenstreich
The #biovoxxel figure tools provide a convenient way in saving SVG vector graphic from Fiji and create publication figures in Inkscape.
Thanks to Ved Sharma those SVGs can now also be opened in the browser and even in Adobe Illustrator, if you really have to use it (I won't blame you 😉)
Thanks to Ved Sharma those SVGs can now also be opened in the browser and even in Adobe Illustrator, if you really have to use it (I won't blame you 😉)
November 20, 2024 at 1:49 PM
The #biovoxxel figure tools provide a convenient way in saving SVG vector graphic from Fiji and create publication figures in Inkscape.
Thanks to Ved Sharma those SVGs can now also be opened in the browser and even in Adobe Illustrator, if you really have to use it (I won't blame you 😉)
Thanks to Ved Sharma those SVGs can now also be opened in the browser and even in Adobe Illustrator, if you really have to use it (I won't blame you 😉)
Reposted by Jacques Augenstreich
Microscopy 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...
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...
January 15, 2025 at 1:39 PM
Microscopy 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...
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
I was looking forward to this one! An open source software for fast reconstruction of 3D structured illumination microscopy (SIM) from Xi Peng's lab : www.cell.com/the-innovati...
Matlab-based, code here: github.com/Cao-ruijie/F...
Matlab-based, code here: github.com/Cao-ruijie/F...
January 13, 2025 at 12:10 PM
I was looking forward to this one! An open source software for fast reconstruction of 3D structured illumination microscopy (SIM) from Xi Peng's lab : www.cell.com/the-innovati...
Matlab-based, code here: github.com/Cao-ruijie/F...
Matlab-based, code here: github.com/Cao-ruijie/F...
Reposted by Jacques Augenstreich
Our fully 3D-printed microscope is featured in @newscientist.bsky.social www.newscientist.com/article/2462...
World’s first fully 3D-printed microscope made in under 3 hours
The microscope cost less than £50 to build using an open-source design and a common 3D printer
www.newscientist.com
January 10, 2025 at 9:44 PM
Our fully 3D-printed microscope is featured in @newscientist.bsky.social www.newscientist.com/article/2462...
Reposted by Jacques Augenstreich
😎 awesome story! A must-read for a cellular-microbiologist working on Mtb! Congrats 🍾
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 👇
(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 👇
Dynamic interplay of autophagy and membrane repair during Mycobacterium tuberculosis Infection
Author summary Autophagy is a cellular process that allows cells to digest internal materials and may help in the defense against pathogenic bacteria, including Mycobacterium tuberculosis (Mtb), the c...
doi.org
January 8, 2025 at 8:28 PM
😎 awesome story! A must-read for a cellular-microbiologist working on Mtb! Congrats 🍾
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 👇
(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 👇
Dynamic interplay of autophagy and membrane repair during Mycobacterium tuberculosis Infection
Author summary Autophagy is a cellular process that allows cells to digest internal materials and may help in the defense against pathogenic bacteria, including Mycobacterium tuberculosis (Mtb), the c...
doi.org
January 8, 2025 at 1:57 PM
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 👇
(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 Augenstreich
Hey #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)?
or when you need to push-back on silly reviewer requests (e.g., asking for p-values in table 1)?
January 6, 2025 at 8:15 AM
Hey #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)?
or when you need to push-back on silly reviewer requests (e.g., asking for p-values in table 1)?