Software, Scripts, and Tutorials

Name & Link	Type	Citation	Details
TomoGuide	Tutorial	Van der Stappen & Waltz 2025	Cryo-ET processing workflow tutorial
ChlamyAnnotations	Dataset annotation	Kelley et al. 2026	Annotation of organelles, particle positions, and scripts for the Chlamy dataset (EMPIAR-11830)
DeepFinder	Software package	Moebel et al. 2021	Deep Learning (DL) particle picking
MemBrain v1	Software package	Lamm et al. 2022	DL membrane particle picking
MemBrain v2	Software package	Lamm et al. 2024	The full MemBrain v2 package
MemBrain-seg	Software package	Lamm et al. 2024	DL membrane segmentation (part of MemBrain v2)
MemBrain-pick	Software package	Lamm et al. 2024	DL membrane particle picking (part of MemBrain v2)
MemBrain-stats	Software package	Lamm et al. 2024	Spatial analysis and statistics on picked particles (part of MemBrain v2)
napari-lasso-3d	Software package	Lamm et al. 2024	Napari plugin to manually cut membrane segmentations
Surforama	Software package	Yamauchi ​et al. 2024	Napari plugin to visualize and pick densities projected on segmented surfaces
Membranorama	Software package	Wietrzynski et al. 2020	Standalone package to visualize and pick densities projected on segmented surfaces
Slabify	Software package	Righetto & Lamm 2024	Lamella slab mask segmentation (manual, semi-automated and fully automated)
ICE-TIDE	Software package	Debarnot et al. 2025	DL tilt-series alignment
CryoLithe	Software package	Kishore et al. 2025	DL supervised 3D reconstruction and denoising
🍦 ICECREAM	Software package	Kishore et al. 2025	DL self-supervised denoising
Stoic	Software package	Litvinov et al. 2026	Stoichiometry prediction of protein complexes
batch_pytom_aretomo3	Script	N/A	Run pytom-match-pick on an AreTomo3 project
aretomo3torelion5	Script	N/A	Import AreTomo3 project into Relion-5
polish2aretomo3	Script	N/A	Import polishing results from Relion-5 into AreTomo3
CellArchLab cryoET-scripts	Script collection	N/A	Miscellaneous scripts to aid cryo-ET data processing, mainly denoising. Also includes `defocusgrad` for defocus handedness estimation.

Public Datasets

Name & Link	Type & Size	Citation	Details
EMPIAR-10694	1 tilt-series	Freeman Rosenzweig et al. 2017	In situ cryo-ET of C. reinhardtii pyrenoid  (WT)
EMPIAR-10680	8120 micrographs	Gupta et al. 2021	Single-particle cryo-EM of VIPP1
EMPIAR-11058	36 tilt-series, 25141 subtomograms	Dietrich et al. 2022	In situ cryo-ET of T. kivui cells
EMPIAR-11078	20 tilt-series, 2923 subtomograms	van den Hoek et al. 2022	In situ cryo-ET of C. reinhardtii ciliary transition zone
EMPIAR-11747	7 tilt-series	Shimakawa et al. 2024	In situ cryo-ET of ​P. tricornutum & T. pseudonana pyrenoids (WT, PyShell1/2 KO)
EMPIAR-12250	15 tilt-series	Nam et al. 2024	In situ cryo-ET of T. pseudonana pyrenoids  ​(PyShell4 KO)
EMPIAR-12612	18 tilt-series, 9 membrane segmentations	Wietrzynski et al. 2025	In situ cryo-ET of spinach chloroplasts
EMPIAR-13055	72 tilt-series	Bertiaux et al. 2025	In situ cryo-ET of the ciliary base in primary mouse epithelial tracheal cells (MTEC)
EMPIAR-11830	1829 tilt-series	Kelley et al. 2026	Large-scale in situ cryo-ET dataset of C. reinhardtii prepared with plasma FIB milling