hamid13r.bsky.social
@hamid13r.bsky.social
Staff Scientist/Grotjahn Lab/Scripps Research
CryoET everything! #TeamTomo
CryoET everything! #TeamTomo
Reposted by hamid13r.bsky.social
#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).
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).
Medina, Chang et al. of the @nanigrotjahn.bsky.social lab introduce a new method based on the Surface Morphometrics pipeline to measure global and local thicknesses of organellar #membranes from cellular cryo-electron tomography data. rupress.org/jcb/article/...
#CryoET
#CryoET
January 6, 2026 at 1:51 AM
#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).
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).
Reposted by hamid13r.bsky.social
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/...
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
rupress.org
December 26, 2025 at 8:21 PM
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/...
Reposted by hamid13r.bsky.social
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...
December 17, 2025 at 4:00 PM
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...
Reposted by hamid13r.bsky.social
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
s/o to co-authors @baradlab.com @hamid13r.bsky.social @zidlab.bsky.social
#teamtomo #cellbio25
@attychang.bsky.social, @nanigrotjahn.bsky.social et al. show that cytoplasmic #ribosomes on #mitochondria alter the local membrane environment for protein import. rupress.org/jcb/article/...
📕 From The Year In Cell Biology: rupress.org/jcb/collecti...
#CellBio2025
📕 From The Year In Cell Biology: rupress.org/jcb/collecti...
#CellBio2025
December 7, 2025 at 8:10 PM
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
s/o to co-authors @baradlab.com @hamid13r.bsky.social @zidlab.bsky.social
#teamtomo #cellbio25
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!
I met Matt Iadanza at the CZI but I guess he doesn't have bluesky to tag!
November 25, 2025 at 6:26 PM
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!
I met Matt Iadanza at the CZI but I guess he doesn't have bluesky to tag!
Reposted by hamid13r.bsky.social
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
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
Prohibitin complexes associate with unique membrane microdomains in cells https://www.biorxiv.org/content/10.1101/2025.11.14.688579v1
November 17, 2025 at 12:22 AM
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
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
Reposted by hamid13r.bsky.social
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
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
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
Prohibitin complexes associate with unique membrane microdomains in cells https://www.biorxiv.org/content/10.1101/2025.11.14.688579v1
November 17, 2025 at 12:33 AM
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
Reposted by hamid13r.bsky.social
Jan-Hannes Schäfer et al.: CryoSift: an accessible and automated CNN-driven tool for cryo-EM 2D class selection ##Automation##DataProcessing##CryoEM@umich...##IUCrhttps://journals.iucr.org/paper?S2053230X25008866
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.
journals.iucr.org
November 8, 2025 at 1:00 AM
Jan-Hannes Schäfer et al.: CryoSift: an accessible and automated CNN-driven tool for cryo-EM 2D class selection ##Automation##DataProcessing##CryoEM@umich...##IUCrhttps://journals.iucr.org/paper?S2053230X25008866
Reposted by hamid13r.bsky.social
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/vx/appcentre...
Quick Check Needed
mrc.tal.net
October 29, 2025 at 9:17 AM
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/vx/appcentre...
Reposted by hamid13r.bsky.social
-80 freezer at -20
In honour of spooky month, share a 4 word horror story that only someone in your profession would understand.
rm -rf ~/
rm -rf ~/
"The chancellor approved it"
October 12, 2025 at 9:56 PM
-80 freezer at -20
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/hamid13r/war...
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 ...
github.com
October 8, 2025 at 10:48 PM
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/hamid13r/war...
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...
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...
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
github.com
October 6, 2025 at 10:51 PM
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...
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...
Reposted by hamid13r.bsky.social
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!
This looks like a fantastic meeting!
Happy to announce "Technical Innovations Using #SerialEM: A Community Meeting", a new format of hybrid meeting David Mastronarde and I are organizing in April 2026. For more info, a preliminary list of speakers, pre-registration etc. visit
www.nexperion.net/semcm2026
www.nexperion.net/semcm2026
September 23, 2025 at 2:09 PM
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!
This looks like a fantastic meeting!
Reposted by hamid13r.bsky.social
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
September 16, 2025 at 3:28 PM
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
Reposted by hamid13r.bsky.social
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...
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...
www.biorxiv.org
August 23, 2025 at 9:18 AM
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...
Ran out of github copilot prompts while programming and realized I was already depending on in too much :(
July 9, 2025 at 6:04 AM
Ran out of github copilot prompts while programming and realized I was already depending on in too much :(
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.
Unfortunately, as an immigrant I would rather not to explain any further.
June 13, 2025 at 3:17 AM
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.
Unfortunately, as an immigrant I would rather not to explain any further.
I LOVE this photo of the Grotjahn Lab. Congrats, Dr. Medina! @mmedina300kv.bsky.social
May 10, 2025 at 3:23 AM
I LOVE this photo of the Grotjahn Lab. Congrats, Dr. Medina! @mmedina300kv.bsky.social
Reposted by hamid13r.bsky.social
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 ☀️⚡
May 10, 2025 at 1:11 AM
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 ☀️⚡
Reposted by hamid13r.bsky.social
Apply to our @PhDposition - deadline this Sunday!
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/
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/
May 2, 2025 at 1:17 PM
Apply to our @PhDposition - deadline this Sunday!
Reposted by hamid13r.bsky.social
🚨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
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
Surface morphometrics reveals local membrane thickness variation in organellar subcompartments https://www.biorxiv.org/content/10.1101/2025.04.30.651574v1
May 1, 2025 at 7:42 PM
🚨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
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
Our badass graduate student @attychang.bsky.social 's paper is on JCB's cover 🥳🥳🥳
Our April issue is here! rupress.org/jcb/issue/22...
The cover shows a segmented model of cytoplasmic #ribosomes associated with mitochondrial membrane in a Saccharomyces cerevisiae cell. From Ya-Ting Chang, @nanigrotjahn.bsky.social and colleagues (doi.org/10.1083/jcb....)
The cover shows a segmented model of cytoplasmic #ribosomes associated with mitochondrial membrane in a Saccharomyces cerevisiae cell. From Ya-Ting Chang, @nanigrotjahn.bsky.social and colleagues (doi.org/10.1083/jcb....)
April 10, 2025 at 3:15 AM
Our badass graduate student @attychang.bsky.social 's paper is on JCB's cover 🥳🥳🥳
Reposted by hamid13r.bsky.social
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/
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/
April 4, 2025 at 8:06 AM
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/
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/
Reposted by hamid13r.bsky.social
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
March 9, 2025 at 5:07 AM
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
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!
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!
Ya-Ting Chang, @nanigrotjahn.bsky.social et al. @scripps.edu present a membrane-guided approach for identifying a subset of cytoplasmic #ribosomes oriented for protein import on the surface of #mitochondria in budding yeast using #cryoET: rupress.org/jcb/article/...
March 8, 2025 at 6:21 AM
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!
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!