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hamid13r.bsky.social

@hamid13r.bsky.social
176 followers 271 following 122 posts

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

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Debnath Ghosal @debnathghosal.bsky.social · 07/10/2026
When imaging at high mag using cryo-ET, field of view reduces. How to overcome this limit? How do we get a "bird’s-eye view" without compromising resolution? Our very own @HamishBrown has a solution to this: “montage tomography with a rectangular beam!” www.biorxiv.org/content/10.6...
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Ben Barad @baradlab.com · 07/10/2026
For #teamtomo folks, I just pushed beta 6 for Surface Morphometrics. We're probably on our second to last beta before 2.0 full release. For adventurous types, check out the `statistics` branch, which has a LOT of new toys that will be coming in the next beta, including yml configurable stats!
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Shervin Nia @shervinnia.bsky.social · 08/10/2026
So excited to finally share my first lead-author paper where we made discoveries about protein crystals and radiation damage using #4DSTEM, and we got the cover thanks to the talented @lenka11.bsky.social!
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hamid13r.bsky.social @hamid13r.bsky.social · 07/10/2026
What do you think of Nouredine Zettili's QM book?
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hamid13r.bsky.social @hamid13r.bsky.social · 07/10/2026
using miss-alignment or MTools) and directly create novaCTF or etomo style tomograms. This would be much faster and will keeps the geo consistency for later work like particle picking or segmentation. github.com/hamid13r/tom...
github.com
GitHub - hamid13r/tomo_toolshed: A small, growing collection of lightweight cryo-ET file/CLI tools focused on the WarpTools pipeline.
A small, growing collection of lightweight cryo-ET file/CLI tools focused on the WarpTools pipeline. - hamid13r/tomo_toolshed
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hamid13r.bsky.social @hamid13r.bsky.social · 07/10/2026
TOMO_TOOLSHED This is still in its earlier stages, but I am putting my scripts together in a github repo (with the help of Claude) and trying to see if I can maintain and improve it. The part I am excited about is the xml-reconstruction, where you can use the xml files (imported and improved /1
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hamid13r.bsky.social @hamid13r.bsky.social · 24/09/2026
Fair enough. Unfortunately, people do need to be reminded of the obvious considerations, especially on "hot" topics of the day.
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hamid13r.bsky.social @hamid13r.bsky.social · 24/09/2026
Isn't that most conservatives + Bill Maher's whole thing? It has been "flying" imo
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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 · 09/09/2026
LOL not her politics per se. I will let you be haha
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hamid13r.bsky.social @hamid13r.bsky.social · 08/09/2026
Friends who phage together, stage togerher?
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hamid13r.bsky.social @hamid13r.bsky.social · 08/09/2026
is that shohre aghdashlou?
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hamid13r.bsky.social @hamid13r.bsky.social · 03/09/2026
yeah it is quite saddening though...
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hamid13r.bsky.social @hamid13r.bsky.social · 02/09/2026
ironically, Dari is less mixed with arabic and a lot of iranians hate the association. but less arabic and more original persian does not make them like Dari more :)))
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hamid13r.bsky.social @hamid13r.bsky.social · 02/09/2026
did your Iranian friend say that or the Hazara friend? Iranians and Americans (of all walks) and so much in common it is getting weird lol
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hamid13r.bsky.social @hamid13r.bsky.social · 02/09/2026
I can "read" arabic script easily (same as Persian) but it quickly gets tricky with unfamiliar/old words... this is also hand-written in a special font etc. also i didnt know Khakhaam that we use in persian is from hebrew and was used here...
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hamid13r.bsky.social @hamid13r.bsky.social · 02/09/2026
Is that Masoud same as مسعود؟
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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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hamid13r.bsky.social @hamid13r.bsky.social · 01/09/2026
Shalom 35, Masoud(?) 48, and Yehuda 30 seem to be brothers (Baghitou or something like that) they are money exchanger (I think), rabbi, and merchant.
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hamid13r.bsky.social @hamid13r.bsky.social · 01/09/2026
Name, age, job, and what?
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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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hamid13r.bsky.social @hamid13r.bsky.social · 23/01/2026
ahhh i have a guess where this is coming from ✋
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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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hamid13r.bsky.social @hamid13r.bsky.social · 23/01/2026
For light and darkness, "allah takes them out of darkness towards light" is a highly repeated phrase in the Quran... even I remembered it without searching... (also, i cannot see the other reply) quran.com/al-baqarah/257
quran.com
Surah Al-Baqarah - 257 - Quran.com
Allah is the Guardian of the believers—He brings them out of darkness and into light. As for the disbelievers, their guardians are false gods who lead...
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hamid13r.bsky.social @hamid13r.bsky.social · 23/01/2026
I did find the title a bit weird, then the account bio cleared it!
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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 · 26/11/2025
Relion GUI is an interesting thing to be attached to 😄
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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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hamid13r.bsky.social @hamid13r.bsky.social · 18/11/2025
Randall Alberto Gamboa Esquivel?
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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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hamid13r.bsky.social @hamid13r.bsky.social · 16/11/2025
"Oh look by the time the bloody night reach the dawn, how many daggers passed through how many hearts... blood of each heart a grew cedar tree, and on each cedar a bird started a singing spree... Echos of blood heard in the song of the bird... oh this in the cedar's blood, remembered"
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hamid13r.bsky.social @hamid13r.bsky.social · 16/11/2025
Yes, also نگر is only used in poets nowadays...
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hamid13r.bsky.social @hamid13r.bsky.social · 16/11/2025
نگر Is short form of "Bengar" meaning "look" (negær) نگار Is the feminine name (negːar)
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hamid13r.bsky.social @hamid13r.bsky.social · 13/11/2025
Why?
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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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hamid13r.bsky.social @hamid13r.bsky.social · 07/11/2025
I didn't know Americans just mass convert a new religion any time they elect a new leader! interesting!
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hamid13r.bsky.social @hamid13r.bsky.social · 04/11/2025
More EMpower to you 🔥
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hamid13r.bsky.social @hamid13r.bsky.social · 01/11/2025
I will look into it, I think i have used it once!
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hamid13r.bsky.social @hamid13r.bsky.social · 01/11/2025
It also might be a little anxiety of "oh this error in installation, is it because they used conda?" Not sure how true is that to be honest...
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hamid13r.bsky.social @hamid13r.bsky.social · 01/11/2025
At first, i kept getting incompatible version problems. Soecially when the developper had specified all versions of all packages, but now it seems conda-forge + micromamba solves all things!
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hamid13r.bsky.social @hamid13r.bsky.social · 01/11/2025
Yeah i have been getting by using micromamba (we have conda blocked completely) but installing package and troubleshooting was so much easier before...
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hamid13r.bsky.social @hamid13r.bsky.social · 01/11/2025
It is also not free 😭
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