In the latest CryoSPARC Blog we walk through the key processing strategies to handle preferred orientation in the tested #EMPIAR datasets. These steps resulted in a smaller, more balanced particle stack, showing that retaining more particles doesn't necessarily translate into a better reconstruction
October 29, 2026 at 12:03 PM
In the latest CryoSPARC Blog we walk through the key processing strategies to handle preferred orientation in the tested #EMPIAR datasets. These steps resulted in a smaller, more balanced particle stack, showing that retaining more particles doesn't necessarily translate into a better reconstruction
The main #cryoEM dataset from this paper is now publicly available! 🎁
www.ebi.ac.uk/empiar/EMPIA...
The other dataset will follow in the coming week or two. It is already deposited but can't be released before the corresponding EMDB entry, which is scheduled for release next week.
www.ebi.ac.uk/empiar/EMPIA...
The other dataset will follow in the coming week or two. It is already deposited but can't be released before the corresponding EMDB entry, which is scheduled for release next week.
EMPIAR-12814 Single-particle cryo-EM dataset of monomeric Photosystem I structure at 1.8 A resolution
EMPIAR, the Electron Microscopy Public Image Archive centered at EMBL-EBI, is a public resource for raw electron
microscopy images related to EMDB, contains micrographs, particle sets and tilt-ser...
www.ebi.ac.uk
October 22, 2026 at 9:22 AM
The main #cryoEM dataset from this paper is now publicly available! 🎁
www.ebi.ac.uk/empiar/EMPIA...
The other dataset will follow in the coming week or two. It is already deposited but can't be released before the corresponding EMDB entry, which is scheduled for release next week.
www.ebi.ac.uk/empiar/EMPIA...
The other dataset will follow in the coming week or two. It is already deposited but can't be released before the corresponding EMDB entry, which is scheduled for release next week.
Nice! ...and the raw data on @emdatabank.bsky.social EMPIAR?
October 13, 2026 at 7:36 PM
Nice! ...and the raw data on @emdatabank.bsky.social EMPIAR?
Caveat being that data was pristine and I was using alignments from EMPIAR
October 11, 2026 at 9:31 AM
Caveat being that data was pristine and I was using alignments from EMPIAR
Curious to see what a malaria parasite looks like during different stages of cytokinesis? 🫣
In this month’s @nfdi4bioimage.bsky.social calendar, we present a dataset of Plasmodium falciparum in EMPIAR and available as OME-Zarr via the @bioimagearchive.bsky.social, both hosted by @ebi.embl.org.
In this month’s @nfdi4bioimage.bsky.social calendar, we present a dataset of Plasmodium falciparum in EMPIAR and available as OME-Zarr via the @bioimagearchive.bsky.social, both hosted by @ebi.embl.org.
October 6, 2026 at 11:37 AM
Curious to see what a malaria parasite looks like during different stages of cytokinesis? 🫣
In this month’s @nfdi4bioimage.bsky.social calendar, we present a dataset of Plasmodium falciparum in EMPIAR and available as OME-Zarr via the @bioimagearchive.bsky.social, both hosted by @ebi.embl.org.
In this month’s @nfdi4bioimage.bsky.social calendar, we present a dataset of Plasmodium falciparum in EMPIAR and available as OME-Zarr via the @bioimagearchive.bsky.social, both hosted by @ebi.embl.org.
Particle picking may be cryoEM's most overlooked step.
We reprocessed a 49 kDa membrane target (EMPIAR-10330) with Topaz Masterclass methods, resulting in:
• 5x particles: 3.2Å ➔ 2.9Å
• Improved side-chain densities (Phe106 in vid)
Learn how: www.cryoarcana.com/topaz-master...
We reprocessed a 49 kDa membrane target (EMPIAR-10330) with Topaz Masterclass methods, resulting in:
• 5x particles: 3.2Å ➔ 2.9Å
• Improved side-chain densities (Phe106 in vid)
Learn how: www.cryoarcana.com/topaz-master...
October 1, 2026 at 10:53 PM
Particle picking may be cryoEM's most overlooked step.
We reprocessed a 49 kDa membrane target (EMPIAR-10330) with Topaz Masterclass methods, resulting in:
• 5x particles: 3.2Å ➔ 2.9Å
• Improved side-chain densities (Phe106 in vid)
Learn how: www.cryoarcana.com/topaz-master...
We reprocessed a 49 kDa membrane target (EMPIAR-10330) with Topaz Masterclass methods, resulting in:
• 5x particles: 3.2Å ➔ 2.9Å
• Improved side-chain densities (Phe106 in vid)
Learn how: www.cryoarcana.com/topaz-master...
New Case Study: We reprocessed a 49 kDa membrane protein (EMPIAR-10330) with optimized Topaz methods.
Results:
• 5x particles: 3.2Å ➔ 2.9Å
• Improved side-chain clarity (Phe106 re-fit in vid)
Learn how - Topaz Masterclass: www.cryoarcana.com/topaz-master...
Results:
• 5x particles: 3.2Å ➔ 2.9Å
• Improved side-chain clarity (Phe106 re-fit in vid)
Learn how - Topaz Masterclass: www.cryoarcana.com/topaz-master...
October 1, 2026 at 10:46 PM
New Case Study: We reprocessed a 49 kDa membrane protein (EMPIAR-10330) with optimized Topaz methods.
Results:
• 5x particles: 3.2Å ➔ 2.9Å
• Improved side-chain clarity (Phe106 re-fit in vid)
Learn how - Topaz Masterclass: www.cryoarcana.com/topaz-master...
Results:
• 5x particles: 3.2Å ➔ 2.9Å
• Improved side-chain clarity (Phe106 re-fit in vid)
Learn how - Topaz Masterclass: www.cryoarcana.com/topaz-master...
Job ID: JR4207
Extract: We are looking for an enthusiastic imaging bioinformatician to support the BioImage Archive and EMPIAR, focusing on data management and community engagement.
Extract: We are looking for an enthusiastic imaging bioinformatician to support the BioImage Archive and EMPIAR, focusing on data management and community engagement.
August 30, 2026 at 8:46 AM
Job ID: JR4207
Extract: We are looking for an enthusiastic imaging bioinformatician to support the BioImage Archive and EMPIAR, focusing on data management and community engagement.
Extract: We are looking for an enthusiastic imaging bioinformatician to support the BioImage Archive and EMPIAR, focusing on data management and community engagement.
Cool microtubule alongside the NE :)))
[Tomogram from EMPIAR-11845]
[Tomogram from EMPIAR-11845]
August 24, 2026 at 11:33 AM
Cool microtubule alongside the NE :)))
[Tomogram from EMPIAR-11845]
[Tomogram from EMPIAR-11845]
🚀 Preprint alert: cFAR and Relative Signal: Diagnosing Preferred Orientation in Single-Particle #CryoEM
Explore how cFAR, tFAR, and Relative Signal provide complementary diagnostics for preferred orientation, tested across 14 #EMPIAR datasets and compared with established metrics 👉 bit.ly/4wBY1Ev
Explore how cFAR, tFAR, and Relative Signal provide complementary diagnostics for preferred orientation, tested across 14 #EMPIAR datasets and compared with established metrics 👉 bit.ly/4wBY1Ev
August 17, 2026 at 12:00 PM
🚀 Preprint alert: cFAR and Relative Signal: Diagnosing Preferred Orientation in Single-Particle #CryoEM
Explore how cFAR, tFAR, and Relative Signal provide complementary diagnostics for preferred orientation, tested across 14 #EMPIAR datasets and compared with established metrics 👉 bit.ly/4wBY1Ev
Explore how cFAR, tFAR, and Relative Signal provide complementary diagnostics for preferred orientation, tested across 14 #EMPIAR datasets and compared with established metrics 👉 bit.ly/4wBY1Ev
We also benchmark our methods against established metrics (including cryoEF, Fourier Shell Occupancy, 3DFSC sphericity, and SCF*) across 14 #EMPIAR datasets and synthetic data, providing a comprehensive evaluation of their strengths and applications.
August 17, 2026 at 12:00 PM
We also benchmark our methods against established metrics (including cryoEF, Fourier Shell Occupancy, 3DFSC sphericity, and SCF*) across 14 #EMPIAR datasets and synthetic data, providing a comprehensive evaluation of their strengths and applications.
We combined the apo and FMRFa-bound FaNaC1 datasets (EMPIAR-11631 and EMPIAR-11632) into a single particle stack, then challenged #CryoSPARC to recover the correct structures.
Along the way, we compare 3D Classification, Heterogeneous Refinement, 3DVA, and 3DFlex.
Along the way, we compare 3D Classification, Heterogeneous Refinement, 3DVA, and 3DFlex.
August 13, 2026 at 4:07 PM
We combined the apo and FMRFa-bound FaNaC1 datasets (EMPIAR-11631 and EMPIAR-11632) into a single particle stack, then challenged #CryoSPARC to recover the correct structures.
Along the way, we compare 3D Classification, Heterogeneous Refinement, 3DVA, and 3DFlex.
Along the way, we compare 3D Classification, Heterogeneous Refinement, 3DVA, and 3DFlex.
Crowd sourcing request!! I'm trialling some dev software and I'm looking for nice public tomograms to use as case studies. Downloading all tomos and looking for good examples is tedious. Can anyone recommend specific tomos from EMPIAR/CZI that have multiple STA targets?
#teamtomo #cryoEM
#teamtomo #cryoEM
December 28, 2025 at 1:38 AM
Also, the nucleosomes in this dataset have been further refined to 4.2 Å resolution (in situ!!!) by the group of Mario Halic:
Improved the nucleosome in cryo-ET dataset EMPIAR-11830 to 4.2 Å resolution, with bulky side chains now visible. | Mario Halic
Improved the nucleosome in cryo-ET dataset EMPIAR-11830 to 4.2 Å resolution, with bulky side chains now visible.
www.linkedin.com
January 9, 2026 at 7:15 PM
Also, the nucleosomes in this dataset have been further refined to 4.2 Å resolution (in situ!!!) by the group of Mario Halic:
#IsoNet2, which can also denoise and correct for the missing wedge, has shown stunning visualizations of our dataset, especially of ATP synthase – without averaging!!!
January 9, 2026 at 7:15 PM
#IsoNet2, which can also denoise and correct for the missing wedge, has shown stunning visualizations of our dataset, especially of ATP synthase – without averaging!!!
To all #ChlamyDataset enthusiasts, here is a script that lets you directly import the pre-processed results from EMPIAR-11830 into #RELION v5 for subtomogram averaging:
github.com/Chromatin-St...
#Chlamydomonas #TeamTomo #CryoET #OpenSoftwareAcceleratesScience
github.com/Chromatin-St...
#Chlamydomonas #TeamTomo #CryoET #OpenSoftwareAcceleratesScience
ChlamyAnnotations/chlamydataset2relion5 at master · Chromatin-Structure-Rhythms-Lab/ChlamyAnnotations
Particle annotations for the large-scale cryo-ET dataset of Chlamydomonas reinhardtii - Chromatin-Structure-Rhythms-Lab/ChlamyAnnotations
github.com
April 28, 2025 at 1:16 PM
To all #ChlamyDataset enthusiasts, here is a script that lets you directly import the pre-processed results from EMPIAR-11830 into #RELION v5 for subtomogram averaging:
github.com/Chromatin-St...
#Chlamydomonas #TeamTomo #CryoET #OpenSoftwareAcceleratesScience
github.com/Chromatin-St...
#Chlamydomonas #TeamTomo #CryoET #OpenSoftwareAcceleratesScience
To conclude, thanks to @cryosagar.bsky.social for the help processing the updates, and to Simone Weyand and Sriram Somasundharam at #EMPIAR for all the assistance in getting it live!
You can also check @cellarchlab.com's thread about the project here 🤩
bsky.app/profile/cell... /END
You can also check @cellarchlab.com's thread about the project here 🤩
bsky.app/profile/cell... /END
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🧵👇
February 28, 2025 at 4:35 PM
To conclude, thanks to @cryosagar.bsky.social for the help processing the updates, and to Simone Weyand and Sriram Somasundharam at #EMPIAR for all the assistance in getting it live!
You can also check @cellarchlab.com's thread about the project here 🤩
bsky.app/profile/cell... /END
You can also check @cellarchlab.com's thread about the project here 🤩
bsky.app/profile/cell... /END
Finally, we have added a STAR file version of the tomolist containing the full metadata, as well as information concerning excluded tilts, defocus, etc as STAR files in each tomogram folder.
Full tomolist:
ftp.ebi.ac.uk/empiar/world...
Correspondence tomo num vs name:
ftp.ebi.ac.uk/empiar/world...
Full tomolist:
ftp.ebi.ac.uk/empiar/world...
Correspondence tomo num vs name:
ftp.ebi.ac.uk/empiar/world...
ftp.ebi.ac.uk
February 28, 2025 at 4:35 PM
Finally, we have added a STAR file version of the tomolist containing the full metadata, as well as information concerning excluded tilts, defocus, etc as STAR files in each tomogram folder.
Full tomolist:
ftp.ebi.ac.uk/empiar/world...
Correspondence tomo num vs name:
ftp.ebi.ac.uk/empiar/world...
Full tomolist:
ftp.ebi.ac.uk/empiar/world...
Correspondence tomo num vs name:
ftp.ebi.ac.uk/empiar/world...
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
hopefully they put the data on EMPIAR so we can all process it
December 19, 2025 at 10:39 AM
hopefully they put the data on EMPIAR so we can all process it