Jess Heebner
@jessheebner.bsky.social
Deep Learning CryoET Image Analysis Specialist, cat lover, dog lover, mother to a 4yo tyrant
Reposted by Jess Heebner
📣 New paper alert! Just out in Cell Reports! pubmed.ncbi.nlm.nih.gov/40644298/
Thrilled to share that we have discovered a brand-new anti-phage defense system! Bacteria have evolved various defense strategies (CRISPR etc) to counter phage attacks. We found a new one - fascinating and dramatic
⚔️🦠❄️🔬
Thrilled to share that we have discovered a brand-new anti-phage defense system! Bacteria have evolved various defense strategies (CRISPR etc) to counter phage attacks. We found a new one - fascinating and dramatic
⚔️🦠❄️🔬
August 2, 2025 at 3:01 PM
📣 New paper alert! Just out in Cell Reports! pubmed.ncbi.nlm.nih.gov/40644298/
Thrilled to share that we have discovered a brand-new anti-phage defense system! Bacteria have evolved various defense strategies (CRISPR etc) to counter phage attacks. We found a new one - fascinating and dramatic
⚔️🦠❄️🔬
Thrilled to share that we have discovered a brand-new anti-phage defense system! Bacteria have evolved various defense strategies (CRISPR etc) to counter phage attacks. We found a new one - fascinating and dramatic
⚔️🦠❄️🔬
Reposted by Jess Heebner
NEW! Hydra Bio Plasma-FIB features AI protocols for bio specimens. Capture high-res 3D data from cryo-preserved or resin-embedded samples & generate high-quality cryo lamellae. Register for June 24 webinar to learn from users how they've enhanced their #volumeEM and #teamtomo prep. ter.li/d8b427
May 30, 2025 at 4:47 PM
NEW! Hydra Bio Plasma-FIB features AI protocols for bio specimens. Capture high-res 3D data from cryo-preserved or resin-embedded samples & generate high-quality cryo lamellae. Register for June 24 webinar to learn from users how they've enhanced their #volumeEM and #teamtomo prep. ter.li/d8b427
Can't wait to try this out! I have loved seeing my segmentations come to life in Blender
In the context of our @reviewcommons.org revision process, I'm happy to announce Microscopy Nodes v2.2.0!
This packs lots of new fun features, including new color management 🌈, clearer transparency handling 🫥, custom default settings 🔧 and more!
Preprint at doi.org/10.1101/2025...
This packs lots of new fun features, including new color management 🌈, clearer transparency handling 🫥, custom default settings 🔧 and more!
Preprint at doi.org/10.1101/2025...
May 23, 2025 at 11:05 PM
Can't wait to try this out! I have loved seeing my segmentations come to life in Blender
Reposted by Jess Heebner
www.wehi.edu.au/careers/make...
WEHI is looking for new lab heads! New and experienced lab heads welcome. Check out the ad, consider applying and share. We’re a collaborative bunch, in Australia, with fabulous technology, great colleagues at a values-driven organisation. @wehi-research.bsky.social
WEHI is looking for new lab heads! New and experienced lab heads welcome. Check out the ad, consider applying and share. We’re a collaborative bunch, in Australia, with fabulous technology, great colleagues at a values-driven organisation. @wehi-research.bsky.social
Make your future Melbourne | WEHI
Lead the next wave of biomedical discovery
www.wehi.edu.au
May 13, 2025 at 11:44 PM
www.wehi.edu.au/careers/make...
WEHI is looking for new lab heads! New and experienced lab heads welcome. Check out the ad, consider applying and share. We’re a collaborative bunch, in Australia, with fabulous technology, great colleagues at a values-driven organisation. @wehi-research.bsky.social
WEHI is looking for new lab heads! New and experienced lab heads welcome. Check out the ad, consider applying and share. We’re a collaborative bunch, in Australia, with fabulous technology, great colleagues at a values-driven organisation. @wehi-research.bsky.social
Reposted by Jess Heebner
Hey #TeamTomo,
Ever been in need of a tutorial about the fundamentals of cryo-electron tomography? From preprocessing raw frames to high-res subtomogram averaging?
That's why @florentwaltz.bsky.social and I made this website!
tomoguide.github.io
Follow the thread 1 /🧵
#CryoET #CryoEM 🔬🧪
Ever been in need of a tutorial about the fundamentals of cryo-electron tomography? From preprocessing raw frames to high-res subtomogram averaging?
That's why @florentwaltz.bsky.social and I made this website!
tomoguide.github.io
Follow the thread 1 /🧵
#CryoET #CryoEM 🔬🧪
Welcome to TomoGuide
A step-by-step Cryo-ET guide
tomoguide.github.io
May 6, 2025 at 4:27 PM
Hey #TeamTomo,
Ever been in need of a tutorial about the fundamentals of cryo-electron tomography? From preprocessing raw frames to high-res subtomogram averaging?
That's why @florentwaltz.bsky.social and I made this website!
tomoguide.github.io
Follow the thread 1 /🧵
#CryoET #CryoEM 🔬🧪
Ever been in need of a tutorial about the fundamentals of cryo-electron tomography? From preprocessing raw frames to high-res subtomogram averaging?
That's why @florentwaltz.bsky.social and I made this website!
tomoguide.github.io
Follow the thread 1 /🧵
#CryoET #CryoEM 🔬🧪
Reposted by Jess Heebner
We have updated our #MemBrain v2 preprint with a lot more details about the MemBrain-pick and MemBrain-stats modules, as well as some application examples!
Stay tuned for the upcoming thread by lead author @lorenzlamm.bsky.social! 🧠🧵
#CryoET #TeamTomo
www.biorxiv.org/content/10.1...
Stay tuned for the upcoming thread by lead author @lorenzlamm.bsky.social! 🧠🧵
#CryoET #TeamTomo
www.biorxiv.org/content/10.1...
April 23, 2025 at 8:47 AM
We have updated our #MemBrain v2 preprint with a lot more details about the MemBrain-pick and MemBrain-stats modules, as well as some application examples!
Stay tuned for the upcoming thread by lead author @lorenzlamm.bsky.social! 🧠🧵
#CryoET #TeamTomo
www.biorxiv.org/content/10.1...
Stay tuned for the upcoming thread by lead author @lorenzlamm.bsky.social! 🧠🧵
#CryoET #TeamTomo
www.biorxiv.org/content/10.1...
Reposted by Jess Heebner
So thrilled to unveil the Krios 5 Cryo-TEM for studying cellular structures and molecular interactions. Thank you to the many, many teammates that made this possible. Watch the video! Watch the more & sign up for virtual event on May 14: ter.li/ueeqfs
www.linkedin.com/posts/thermo...
www.linkedin.com/posts/thermo...
Introducing the Krios 5 Cryo-Transmission Electron Microscope | Thermo Fisher Scientific
Today, we introduce the Krios 5 Cryo-Transmission Electron Microscope, which provides atomic-level insights to help scientists study how cells, proteins and viruses work. Its enhanced optics and new A...
www.linkedin.com
April 2, 2025 at 1:30 PM
So thrilled to unveil the Krios 5 Cryo-TEM for studying cellular structures and molecular interactions. Thank you to the many, many teammates that made this possible. Watch the video! Watch the more & sign up for virtual event on May 14: ter.li/ueeqfs
www.linkedin.com/posts/thermo...
www.linkedin.com/posts/thermo...
Reposted by Jess Heebner
We're on the cover of @science.org this week. Awesome work by @florentwaltz.bsky.social. #CryoET is reaching crazy resolutions inside cells, and this is just the beginning. Fantastic interpretation of the proton motive force by @verenaresch.bsky.social. Always a pleasure making #SciArt with you!🧪🧶🧬🌾
In a new Science study, cryo–electron tomography captures the in-cell architecture of the mitochondrial respiratory chain, illuminating how the coordinated action of molecular machines drives life’s fundamental energy conversion.
Learn more in this week's issue: scim.ag/3FA3Ygq
Learn more in this week's issue: scim.ag/3FA3Ygq
March 20, 2025 at 10:37 PM
We're on the cover of @science.org this week. Awesome work by @florentwaltz.bsky.social. #CryoET is reaching crazy resolutions inside cells, and this is just the beginning. Fantastic interpretation of the proton motive force by @verenaresch.bsky.social. Always a pleasure making #SciArt with you!🧪🧶🧬🌾
Things always get worse before they get better..something something pithy... I'm reposting this because the situation has become more urgent and exponentially more stressful. <3
This week, about a month before I'm moving my entire family to safety in a new state, I was let go from my job, very unexpectedly. So I have a renewed need for donations, and welcome any and all boosts and shares. I'll have follow up posts for my job hunt. gofund.me/9c102eab
Donate to Urgent Move for Our Trans Kid's Safety, organized by Winston Hearn
Update, 3/5/25: This week I was let go from my job very unexpectedly, so this fun… Winston Hearn needs your support for Urgent Move for Our Trans Kid's Safety
gofund.me
March 6, 2025 at 1:18 AM
Things always get worse before they get better..something something pithy... I'm reposting this because the situation has become more urgent and exponentially more stressful. <3
Reposted by Jess Heebner
To all #TeamTomo #CryoET and #Chlamydomonas aficionados: we have updated EMPIAR-11830 with a bug fix concerning some cryo-CARE denoised tomos as well as additional files and metadata! 🎉👩🏽💻
www.ebi.ac.uk/empiar/EMPIA...
A little thread about what's new... 🧵 1/n
www.ebi.ac.uk/empiar/EMPIA...
A little thread about what's new... 🧵 1/n
February 28, 2025 at 4:35 PM
To all #TeamTomo #CryoET and #Chlamydomonas aficionados: we have updated EMPIAR-11830 with a bug fix concerning some cryo-CARE denoised tomos as well as additional files and metadata! 🎉👩🏽💻
www.ebi.ac.uk/empiar/EMPIA...
A little thread about what's new... 🧵 1/n
www.ebi.ac.uk/empiar/EMPIA...
A little thread about what's new... 🧵 1/n
Excited to see this out!!
Training Generalized Segmentation Networks with Real and Synthetic Cryo-ET data. [new]
Simulated cryo-ET data trains initial segmentation models. Real data & co-training improve network generality.
Simulated cryo-ET data trains initial segmentation models. Real data & co-training improve network generality.
February 5, 2025 at 2:09 PM
Excited to see this out!!
I typically stick to science/cryoem posts here, but this is very important to me as this is my brother and his family. I want to see them safe. <3
There was a time in my life when I felt extremely bad asking for help, but that time is well past. The government is actively trying to kill my kid, and I would like a little support as I get us (including my ex-wife and her partner) to safety. Thanks! gofund.me/60443e5c
Donate to Urgent Move for Our Trans Kid's Safety, organized by Winston Hearn
Hi! We’re divorced coparents raising money to defray the costs of moving our two … Winston Hearn needs your support for Urgent Move for Our Trans Kid's Safety
gofund.me
February 4, 2025 at 1:31 AM
I typically stick to science/cryoem posts here, but this is very important to me as this is my brother and his family. I want to see them safe. <3
Reposted by Jess Heebner
Finally out! Working with this team was a fantastic learning experience. Also I was excited to determine the in situ clathrin structure for this project! That’s my first EM-structure upload to EMDB. Can I tell my mom I am a structural biologist now? 😁 #cryoET
January 6, 2025 at 6:00 PM
Finally out! Working with this team was a fantastic learning experience. Also I was excited to determine the in situ clathrin structure for this project! That’s my first EM-structure upload to EMDB. Can I tell my mom I am a structural biologist now? 😁 #cryoET
Reposted by Jess Heebner
Thanks Alicia! I am also happy to have helped finalize this work. I hope computational biologists will find the repo useful. We need to share more annotations in accessible format, the algorithms are hungry 😄 #teamtomo, consider sharing your data via pull requests—let’s grow this together! 🤝
I am happy to be a part of this effort and looking forward to the discoveries this dataset will enable! If you work with this dataset in the future, please add any annotations to the GitHub repository github.com/Chromatin-St... Thanks @paloha.bsky.social for spearheading the efforts with this!
January 7, 2025 at 1:18 PM
Thanks Alicia! I am also happy to have helped finalize this work. I hope computational biologists will find the repo useful. We need to share more annotations in accessible format, the algorithms are hungry 😄 #teamtomo, consider sharing your data via pull requests—let’s grow this together! 🤝
Excited to finally get to share the segmentations I've been doing for this project! Eventually I'll get all 1829 tomograms segmented as fully as I can. But.... long term project. For now I'm just excited to see it out in the wild!
Towards community-driven visual proteomics! Excited to finally share this large-scale curated & annotated dataset of 1829 high-quality #cryoET tomograms of the little green alga that just keeps giving— Chlamydomonas! 🧪🧶🧬🌾🌊🌍
Preprint📜: www.biorxiv.org/content/10.1...
A short thread🧵👇
Preprint📜: www.biorxiv.org/content/10.1...
A short thread🧵👇
January 6, 2025 at 2:05 PM
Excited to finally get to share the segmentations I've been doing for this project! Eventually I'll get all 1829 tomograms segmented as fully as I can. But.... long term project. For now I'm just excited to see it out in the wild!
Reposted by Jess Heebner
Check this out, maybe your last read of the year, or the first for the next one 📖?
We used Chlamydomonas 🦠 to push cellular tomography towards the next step and made all the data public!
BTW it's the same dataset I used for the mitochondrial respirasomes www.biorxiv.org/content/10.1...
Enjoy 🥳!
We used Chlamydomonas 🦠 to push cellular tomography towards the next step and made all the data public!
BTW it's the same dataset I used for the mitochondrial respirasomes www.biorxiv.org/content/10.1...
Enjoy 🥳!
December 30, 2024 at 9:58 AM
Check this out, maybe your last read of the year, or the first for the next one 📖?
We used Chlamydomonas 🦠 to push cellular tomography towards the next step and made all the data public!
BTW it's the same dataset I used for the mitochondrial respirasomes www.biorxiv.org/content/10.1...
Enjoy 🥳!
We used Chlamydomonas 🦠 to push cellular tomography towards the next step and made all the data public!
BTW it's the same dataset I used for the mitochondrial respirasomes www.biorxiv.org/content/10.1...
Enjoy 🥳!
Reposted by Jess Heebner
More than 1'800 tomograms available for the community. Towards visual proteomics using our favorite organism Chlamy!
Check out the preprint: www.biorxiv.org/content/10.1...
Find it on EMPIAR (11830) and fully annotated on the CZI data portal: cryoetdataportal.czscience.com
#TeamTomo
Check out the preprint: www.biorxiv.org/content/10.1...
Find it on EMPIAR (11830) and fully annotated on the CZI data portal: cryoetdataportal.czscience.com
#TeamTomo
Towards community-driven visual proteomics with large-scale cryo-electron tomography of Chlamydomonas reinhardtii
In situ cryo-electron tomography (cryo-ET) has emerged as the method of choice to investigate structures of biomolecules in their native context. However, challenges remain in the efficient production...
www.biorxiv.org
December 29, 2024 at 11:47 AM
More than 1'800 tomograms available for the community. Towards visual proteomics using our favorite organism Chlamy!
Check out the preprint: www.biorxiv.org/content/10.1...
Find it on EMPIAR (11830) and fully annotated on the CZI data portal: cryoetdataportal.czscience.com
#TeamTomo
Check out the preprint: www.biorxiv.org/content/10.1...
Find it on EMPIAR (11830) and fully annotated on the CZI data portal: cryoetdataportal.czscience.com
#TeamTomo
Reposted by Jess Heebner
Post-Doc Position WANTED⚡️
I'll finish my PhD work within the next few month and started to sort out where to continue doing exciting science. Any recommendations & suggestions are welcome🙏 More information on my scientific background and ideas for the future below 🧵 reskeet very much appreciated!
I'll finish my PhD work within the next few month and started to sort out where to continue doing exciting science. Any recommendations & suggestions are welcome🙏 More information on my scientific background and ideas for the future below 🧵 reskeet very much appreciated!
December 22, 2024 at 6:21 AM
Post-Doc Position WANTED⚡️
I'll finish my PhD work within the next few month and started to sort out where to continue doing exciting science. Any recommendations & suggestions are welcome🙏 More information on my scientific background and ideas for the future below 🧵 reskeet very much appreciated!
I'll finish my PhD work within the next few month and started to sort out where to continue doing exciting science. Any recommendations & suggestions are welcome🙏 More information on my scientific background and ideas for the future below 🧵 reskeet very much appreciated!
Reposted by Jess Heebner
Proudly present our new preprint on my first post here. We performed SPA on the ciliary tip and identify 7 proteins. Among them, we found the conserved protein SPEF1 at the microtubule seam. In vitro assays show that SPEF1 binds to the seam and stablizes microtubules.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
December 8, 2024 at 5:39 PM
Coming to #ASCB2023? I'd love to chat! Come to my talk in the Deep Learning and AI in Cell Imaging subgroup on Saturday at 1pm (Room 253B) or stop by my poster (B4) on Tuesday at 1:45 onwards.
November 28, 2023 at 5:53 PM
Coming to #ASCB2023? I'd love to chat! Come to my talk in the Deep Learning and AI in Cell Imaging subgroup on Saturday at 1pm (Room 253B) or stop by my poster (B4) on Tuesday at 1:45 onwards.
First post! Imagine segmenting this by hand! This took about 30 minutes to make the training data, only 30 minutes to train and 20 minutes to segment. Data is Empiar 10694 and the network is a Pretrained 2.5D UNet from www.theobjects.com
youtube.com/watch?v=4kb9...
youtube.com/watch?v=4kb9...
Empiar 10694
youtube.com
August 29, 2023 at 3:44 PM
First post! Imagine segmenting this by hand! This took about 30 minutes to make the training data, only 30 minutes to train and 20 minutes to segment. Data is Empiar 10694 and the network is a Pretrained 2.5D UNet from www.theobjects.com
youtube.com/watch?v=4kb9...
youtube.com/watch?v=4kb9...