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hamid13r.bsky.social

@hamid13r.bsky.social
174 followers 269 following 119 posts

Staff Scientist/Grotjahn Lab/Scripps Research CryoET everything! #TeamTomo

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Sergey Ovchinnikov @sokrypton.org · 14/09/2026
Finally a more intuitaive way to learn pLDDT/pAE? 😎 sokrypton.github.io/protein_figh... (Character idea from @hannes-stark.bsky.social & Alex Waldherr)
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Ben Engel @cellarchlab.com · 08/09/2026
MemBrain v2 is on @natmethods.nature.com now? I never had a @biorxivpreprint.bsky.social with 164 citations before😅 ...Which is also to say: Thank you to the amazing #TeamTomo community, many of whom not only beta tested, but also contributed diverse training data. This one belongs to all of us! 🤗🔬🧪
BioRxiv FTW
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hamid13r.bsky.social @hamid13r.bsky.social · 01/09/2026
Really excited to see the square-aperture tiles turned into very large tomograms! github.com/hamid13r/sqa...
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Ben Barad @baradlab.com · 08/07/2026
My personal summer of code continues with another ChimeraX plugin - this time, MorphometricsX! Load quantified meshes from morphometrics (or pycurv) in ChimeraX with color-by-quantification and display alongside tomos and particles. Coming to the toolshed soon! #teamtomo github.com/baradlab/mor...
Screenshot of MorphometricsX rendering mitochondrial membrane surfaces in chimera with color-by-quantification.
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Nature Methods @natmethods.nature.com · 24/08/2026
A Kaggle challenge for particle picking in cryo-ET data spurred the development of new algorithms that outperform state of the art software. www.nature.com/articles/s41...
nature.com
Lessons learned from a Kaggle challenge for particle picking in cryo-electron tomography - Nature Methods
A Kaggle challenge for particle picking in experimental cryo-electron tomography data delivered new machine learning algorithms that outperformed state-of-the-art software and provides a critical refe...
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Nitish Dua @nitishdua.bsky.social · 27/06/2026
Really hyped to share our pre-print on mtDNA replication-fission ! @nanigrotjahn.bsky.social (doi: doi.org/10.64898/202...) 🧵with details below ⤵️
doi.org
ATAD3A structurally links mtDNA replication and mitochondrial fission
Mitochondrial function depends on the maintenance of its genome, and disruptions in copy number and distribution are hallmarks of mitochondrial disorders. Mitochondrial DNA (mtDNA) replication is spat...
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Brian Cook @bcryo.bsky.social · 23/03/2026
1) The Herzik lab is excited to announce our newest preprint in collaboration with the Grotjahn lab! We have developed a surfactant cocktail that seeks to overcome one of the more nefarious problems in #cryoEM, Air-water interface (AWI)-induced damage and preferred orientation (PO).
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Hanjin Liu @liu-hanjin.bsky.social · 22/02/2026
Since last year, I've been making a RELION GUI that supports viewing, navigating and running jobs in a way completely compatible with the original RELION pipeline. Now it's working nicely for both SPA and tomography! Please try it out - github.com/hanjinliu/hi...
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Danielle Grotjahn @nanigrotjahn.bsky.social · 06/01/2026
#teamtomo gets another quantitative cell biology tool! We extend our Surface Morphometrics pipeline to measure membrane thickness. Alongside many biological findings, we show that our 3D measurements closely match in vitro vesicle measurements from 2D EM (collab w/Neal Waxham and Fred Heberle).
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Ben Barad @baradlab.com · 26/12/2025
Online today, the journal version of our ( @nanigrotjahn.bsky.social @attychang.bsky.social @mmedina300kv.bsky.social) manuscript from earlier this year describing membrane thickness measurement in cells with #teamtomo! rupress.org/jcb/article/...
rupress.org
Surface Morphometrics reveals local membrane thickness variation in organellar subcompartments | Journal of Cell Biology | Rockefeller University Press
Medina, Chang et al. introduce a new method based on the Surface Morphometrics pipeline to measure global and local thicknesses of organellar membranes fro
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Jan-Hannes Schaefer @jhschaef.bsky.social · 17/12/2025
In our new preprint, we show how fibril-dynamics of signaling component TIRAP supports sensitive & fast sensing of endotoxin LPS. Congrats to co-lead @arthurfelker.bsky.social. @piehlerlab.bsky.social @arnemoeller.bsky.social #TLR #cryoEM #blender doi.org/10.64898/202...
Blender rendering of TLR4 in membrane and TIRAP fibrils at the plamsma membrane. Blender rendering of TLR4 in membrane and TIRAP fibrils at the plamsma membrane. View from the cytosol.
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Danielle Grotjahn @nanigrotjahn.bsky.social · 07/12/2025
What an honor to see @attychang.bsky.social’s work featured in @jcb.org The Year in Cell Biology 2025 collection! Even more special that it coincides with my first #cellbio2025 conference 🙂 s/o to co-authors @baradlab.com @hamid13r.bsky.social @zidlab.bsky.social #teamtomo #cellbio25
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hamid13r.bsky.social @hamid13r.bsky.social · 25/11/2025
Just installed Doppio on our Linux machine. This is awesome work making relion more accessible and easy to run. I haven't tried submitting jobs yet but it is already making our live easier! I met Matt Iadanza at the CZI but I guess he doesn't have bluesky to tag!
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Danielle Grotjahn @nanigrotjahn.bsky.social · 17/11/2025
Prohibitins aren’t hanging out just anywhere in the membrane — they prefer the 💁‍♀️💎✨VIP section💅🪩🥂 Lab all-star @mmedina300kv.bsky.social maps these microdomains using cryo-ET + surface morphometrics. s/o to #teamtomo #cryoET co-authors @hamid13r.bsky.social @attychang.bsky.social @baradlab.com
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Michaela Medina @mmedina300kv.bsky.social · 17/11/2025
So excited that this work is out and I am so grateful to our team @hamid13r.bsky.social @attychang.bsky.social @baradlab.com @nanigrotjahn.bsky.social
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Structural Biology Communications @actacrystf.iucr.org · 08/11/2025
Jan-Hannes Schäfer et al.: CryoSift: an accessible and automated CNN-driven tool for cryo-EM 2D class selection #Automation #DataProcessing #CryoEM @umich...#IUCr journals.iucr.org/paper?S2053230X25…
journals.iucr.org
CryoSift: an accessible and automated CNN-driven tool for cryo-EM 2D class selection
CryoSift is a CNN-based tool that assesses the quality of 2D class averages. The incorporation of CryoSift into cryoSPARC workflows enables automated particle-stack cleaning.
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Sjors Scheres @sjorsscheres.bsky.social · 29/10/2025
We are looking for a computational postdoc to work with us on new optimisation algorithms to make #RELION even better. Join our bubbly team at the @mrclmb.bsky.social in Cambridge, UK. 🤗 RTs appreciated. mrc.tal.net/vx/appcentre...
mrc.tal.net
Quick Check Needed
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Karen Fisher, PhD @fisherke.bsky.social · 12/10/2025
-80 freezer at -20
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hamid13r.bsky.social @hamid13r.bsky.social · 08/10/2025
I used this opportunity (and github copilot!) to turn this into my first github repository with README and examples, etc. This was a lot of fun! Hopefully, I didn't completely mess it up! github.com/hamid13r/war...
github.com
GitHub - hamid13r/warp_remove_skipped_views: Removing etomo skipped views from Warp xml files to improve the tomogram reconstruction.
Removing etomo skipped views from Warp xml files to improve the tomogram reconstruction. - GitHub - hamid13r/warp_remove_skipped_views: Removing etomo skipped views from Warp xml files to improve ...
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hamid13r.bsky.social @hamid13r.bsky.social · 06/10/2025
Working on #WarpTools I have the old problem of removing "bad tilts". These are views that I skipped in #etomo to get a better model... I wrote a python code to turn the UseTilt to False in the XML files for those views and improve the tomo reconstruction. #teamtomo github.com/hamid13r/war...
github.com
warp_lamella_adapters/remove_bad_views.py at main · hamid13r/warp_lamella_adapters
A short optimized pipeline to get lamella tomography (with pretilt and with some tilts obscured or mistracked) to work well with Warp - hamid13r/warp_lamella_adapters
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Alister Burt @alisterburt.bsky.social · 23/09/2025
The SerialEM Python interface has been a huge driver of innovation at the hardware-software boundary in cryo-EM: suddenly the scientist with some programming chops can readily implement their ideas 🥰 This looks like a fantastic meeting!
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Dovile Januliene @djanuliene.bsky.social · 16/09/2025
We all love colours, especially, when they can be generated automatically! Fantastic talk by Danielle Grotjahn @nanigrotjahn.bsky.social linking method development, structural biology and cell biology! #WEHeraeusSeminar #cryoEM #StructuralBiology #Microscopy @arnemoeller.bsky.social
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Jan Philipp Kreysing @jpkreysing.bsky.social · 23/08/2025
More great cryo-ET benchmarking work from my colleagues Maarten Tuijtel, Tomáš Majtner, Beata Turoňová, & @becklab.bsky.social: Systematic study of how tilt increment choice affects downstream TM & STA. Preprint has the optimally balanced tilt increment. #TeamTomo www.biorxiv.org/content/10.1...
biorxiv.org
Optimal tilt-increment for cryo-ET
Cryo-electron tomography (cryo-ET) enables high-resolution, three-dimensional imaging of cellular structures in their native, frozen state. However, image quality is limited by a trade-off between ang...
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hamid13r.bsky.social @hamid13r.bsky.social · 09/07/2025
Ran out of github copilot prompts while programming and realized I was already depending on in too much :(
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hamid13r.bsky.social @hamid13r.bsky.social · 13/06/2025
It has been an excellent year to be an Iranian scientist working in US academia. Unfortunately, as an immigrant I would rather not to explain any further.
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hamid13r.bsky.social @hamid13r.bsky.social · 10/05/2025
I LOVE this photo of the Grotjahn Lab. Congrats, Dr. Medina! @mmedina300kv.bsky.social
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Danielle Grotjahn @nanigrotjahn.bsky.social · 10/05/2025
It’s been a big week for the Grotjahn Lab—our very first graduate student, @mmedina300kv.bsky.social, successfully defended her PhD thesis! 🎉 So proud of everything she’s accomplished and grateful for the light she’s brought to our lab from day one ☀️⚡
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Lars-Anders Carlson @lacarlson.bsky.social · 02/05/2025
Apply to our @PhDposition - deadline this Sunday!
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Danielle Grotjahn @nanigrotjahn.bsky.social · 01/05/2025
🚨New preprint!🚨 #teamtomo We expanded Surface Morphometrics to quantify membrane thickness from cryo-ET—revealing local variation across organelles. Led by the lab’s first grad student, @mmedina300kv.bsky.social (defending Monday! 🍾) w/ @attychang.bsky.social @hamid13r.bsky.social & @tomo.science
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hamid13r.bsky.social @hamid13r.bsky.social · 10/04/2025
Our badass graduate student @attychang.bsky.social 's paper is on JCB's cover 🥳🥳🥳
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Lars-Anders Carlson @lacarlson.bsky.social · 04/04/2025
Repost appreciated: Open #PhDposition in structural virology in my group! Join us in Umeå, 🇸🇪 to uncover how arboviruses remodel the cellular interior. In situ #cryoET combined with #virology, #cellbiology, and #biophysics. Deadline 4 May. More info: www.carlsonlab.se/join/
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Ardem Patapoutian @ardemp.bskyverified.social · 09/03/2025
Imagine this: The same young scientists now trying to get into PhD programs, facing reduced admissions and uncertainty over whether labs can take them on due to NIH funding cuts, also survived high school during peak COVID and navigated college through a pandemic. 😥😒 #standupforscience
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hamid13r.bsky.social @hamid13r.bsky.social · 08/03/2025
I was trying to explain Grotjahn Lab's research to a friend of mine and was struggling to explain the balance of resolution and context. Suddenly, I remembered Atty's paper: Not only we can locate the ribosomes, we can see their orientations, on the surface of the mitochondria outer membrane!
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Danielle Grotjahn @nanigrotjahn.bsky.social · 07/03/2025
For #teamtomo, context is everything. We highlight the power of #surfacemorphometrics in guiding STA and quantitatively assessing the impact of these structures on the local environment. 1st collab paper w/ @zidlab.bsky.social (hopefully many more to come!) @tomo.science @hamid13r.bsky.social
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Lander Lab @landerlab.bsky.social · 03/03/2025
Congrats to our postdoc Jan-Hannes Schaefer @jhschaef.bsky.social on being awarded a fellowship from the Walter Benjamin Program! Jan is collaborating with the Kelly lab here at Scripps Research @scripps.edu to understand how transthyretin forms amyloids that lead to heart disease.
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Danielle Grotjahn @nanigrotjahn.bsky.social · 14/02/2025
🚨Members of #teamtomo!🚨 We invite you to submit abstracts to our ❄️🔬Cryo-electron Tomography: Progress and Potential session at Microscopy & Microanalysis (M&M) 2025! sample prep, data processing, structural biology, cell biology —we want to hear from you! DEADLINE: February 18 @tomo.science
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Keren Lasker @kerenlasker.bsky.social · 30/12/2024
1/ 🚨We’re thrilled to share our latest study: "Cellular Function of a Biomolecular Condensate Is Determined by Its Ultrastructure" 🌟 www.biorxiv.org/content/10.1... How do biomolecular condensates achieve their cellular roles? It comes down to their internal structure. 🧵⬇️
biorxiv.org
Cellular Function of a Biomolecular Condensate Is Determined by Its Ultrastructure
Biomolecular condensates play key roles in the spatiotemporal regulation of cellular processes. Yet, the relationship between atomic features and condensate function remains poorly understood. We stud...
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Reika Watanabe @reikawatanabe.bsky.social · 24/12/2024
Hello, old and new friends in Bluesky. Using cryo-FIB-ET, we revealed a 9Å structure, identifying novel layers and conserved interfaces that may serve as antiviral targets. #Ebola #Virology #StructuralBiology The full manuscript is available here authors.elsevier.com/sd/article/S...
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Ben Barad @baradlab.com · 16/12/2024
Tomorrow(!) morning at 9AM pacific, I am giving a webinar for EMS discussing the surface morphometrics pipeline and our approach to contextual structural biology #teamtomo. Free to attend, hope to see you all there! us06web.zoom.us/webinar/regi...
Example series showing the surface morphometrics workflow
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hamid13r.bsky.social @hamid13r.bsky.social · 17/12/2024
Yaaaaaaaaayyyy!
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hamid13r.bsky.social @hamid13r.bsky.social · 09/12/2024
There is a very nice feeling to walk a grid directly from aquilos to krios! Almost like an offering to the Krios the god of stars! #cryoET
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Ardem Patapoutian @ardemp.bskyverified.social · 07/12/2024
Ron Milligan, a retired @scripps.edu prof and a pioneer in using cryoEM to advance cell biology, now crafts ceramics—and he’s really good at it! Visited him today and picked up two stunning pieces for my office. One of them will be full of candy, so swing by! 🍬 www.ronmilliganceramics.com/philosophy
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hamid13r.bsky.social @hamid13r.bsky.social · 06/12/2024
My avocado plant has become a very successful algea farm!
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Bui Lab @McGill @builab.bsky.social · 12/05/2022
Just update the subtomo2Chimera withto visualize subtomo from Dynamo. Also, small fixes for relionsubtomo2ChimeraX. now you can also using stl file for visualization for more efficient memory #TeamTomo github.com/builab/subtomo… dynamotable2ChimeraX.py
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Jess Heebner @jessheebner.bsky.social · 01/12/2024
Anyone have any publicly available data (or data you want to share with me) that you'd love to see segmented? I find myself in need of some fun data to segment in my free time... #cryoET or #volumeEM!
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Richard Held @rgsheld.bsky.social · 26/11/2024
Is there such thing as TEMTuesday? Maybe CryoETuesday? Myelinated axon cross section with microtubules and intermediate filaments:
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hamid13r.bsky.social @hamid13r.bsky.social · 23/11/2024
Pottery was an amazing exercise on being "centered" 😄
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Ben Engel @cellarchlab.com · 21/07/2022
Excited to share our new study with the Müller and @SchullerJm labs, online @nature: www.nature.com/articles/s41586-022-… This is T. kivui, an anaerobic bacterium. It uses hydrogen energy to store #CO2. How does it do it? #CryoET revealed membrane-anchored bundles of...
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hamid13r.bsky.social @hamid13r.bsky.social · 20/11/2024
Why do I like seeing actin filaments in my tomograms so much? - bunch of actins passing by in between two mitos in a dendrite! #cryoEM #cryoET #TeamTomo
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Alexis Rohou @alexisrohou.bsky.social · 18/11/2024
🚨 Attention #teamtomo PhD students! 🚨 12-week paid internship opportunity at Genentech. Want to see how we use cryoET in pharma? And spend the summer 2025 in the Bay Area? Details and application link here: roche.wd3.myworkdayjobs.com/ROG-A2O-GENE...
roche.wd3.myworkdayjobs.com
2025 Summer Intern - Department of Structural Biology
Department Summary The CryoEM Group in the Department of Structural Biology is dedicated to providing high-resolution structural insights into biological macromolecules involved in health and disease....
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