Jess Heebner

If you're passionate about #SciArt and #SciComm, don't miss our exciting session today at #ASCB #CellBio2025! Thank you @ascbiology.bsky.social!

Do I need to go fill you a box from this hah

What are your plans for #cellbio2025 ? Aside from eating too much at Reading Terminal Market and wandering the Christmas Market in my spare time... Come find me to chat all things segmentation (and come see my work displayed along the back wall of the Thermo Fisher booth!)

Going to #ASCB2025 in Philly? Come find me! I'll be haunting the Thermo Fisher booth and wandering the conference. I'd love love love to talk all things segmentation! Let's get coffee. Show me your data. Reach out!

This is pretty prevalent in how people communicate science in talks too. So many talks at conferences are just so stilted and dry and they don't have to be. You can communicate complicated topics accessibly to even other experts. But in my experience it's not taught well or at all in school.

I'll be there all conference!

📣 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
⚔️🦠❄️🔬

Sounds like you need a spreadsheet organization system too...

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

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

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 🔬🧪

Figure 4. MemBrain v2 end-to-end workflow detects periodic phycobilisome organization. A: Raw tomogram slice of EMD-31244. B: Out-of-the-box MemBrain-seg segmentation (light blue). C: A single membrane instance can be visualized in Surforama and manually annotated with GT phycobilisome positions (magenta). D: MemBrain-pick localizes particles (trained with data from C) on all membranes in the tomogram. E: MemBrain-stats computes Ripley’s O statistic using the positions from D with a bin size of 5nm. The distance between peaks (35 nm) was measured to estimate chain unit spacings.

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...

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...

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...

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!🧪🧶🧬🌾

What a gorgeous animation!

When I was in grad school I would have loved to learn about roles for bioimage analysis outside of academia because I was struggling to figure out a career path for myself. So personally I'd find it interesting to include stuff like that in the panel!

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

I'm in the process of segmenting all of the tomograms as well! We should look into the best way for sure!

Rare cellular events observed in the cryo-ET dataset. Slices through tomograms (left) with corresponding 3D segmentation (middle and right). Right panels show enlarged views of the boxed regions in the middle panels. A) Mitochondrion at the plasma membrane, tethered to microtubules by thin filaments of unknown identity. Segmented classes: nuclear envelope (light blue), nuclear pore complex (dark blue), 80S ribosomes (orange), mitochondrial membranes (dark red), ATP synthase (royal blue), plasma membranes (grey), microtubules (pink), filaments (yellow), endoplasmic reticulum (purple). Zoomed-in panel shows thin filaments running between microtubules and the mitochondrion at the plasma membrane. Note that this tomogram contains two closely appressed cells, and thus, two plasma membranes with cell walls between. B) Mitochondrial fission event with ER membrane interactions. Segmented classes: mitochondrial membranes (dark red), ATP synthase (royal blue), 80S ribosomes (orange), thylakoid membranes (green), PSII (bright yellow), cell wall (grey), ER (purple), fission site containing filamentous structures perpendicular to the mitochondrial long axis (pale yellow). C) Ciliary transition zone between basal body and axoneme, including assembling IFT train and stellate structure77. Segmented classes: microtubule doublets (light blue), central microtubule pair (light green), stellate structure (pale red), IFT train (yellow). D) Pyrenoid tubule extending from the thylakoids into the phase-separated Rubisco matrix of the pyrenoid. Minitubules originate from thylakoid membranes82. Segmented classes: thylakoid membranes (dark green), PSII (yellow), pyrenoid tubule (lime green), Rubisco (lavender blue), minitubules (orange). Scale bars in A-D: 100 nm. Related to Fig. 2C-H.

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

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

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

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!

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 🥳!

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...

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

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!

Deep Learning-Based Segmentation of Cryo-Electron Tomograms Watch this Scientific Journal Video about Deep Learning-Based Segmentation of Cryo-Electron Tomograms at JoVE.com

Absolutely! I'm most proficient with using Dragonfly and I've written a protocol for my general workflow here. I also use Amira and the open source tool Membrain Seg! Feel free to DM me if you have questions! bit.ly/3ZNpxlj

tagging #CryoEM #CryoET #TeamTomo