Ricardo D. Righetto
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lifeonthewedge.bsky.social
Ricardo D. Righetto
@lifeonthewedge.bsky.social
500 followers 810 following 130 posts
Staff scientist @biozentrum.unibas.ch using algorithms to look at tiny stuff inside cells, or #cryoET if you prefer. Here I talk mostly about my research. Views my own. 🇧🇷 in 🇨🇭
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lifeonthewedge.bsky.social
Like cryo-CARE and DDW, Icecream🍧is a post-processing tool that requires ODD/EVEN tomograms generated from the split of raw movie frames, which are now super easy to obtain e.g. from IMOD alignframes or AreTomo3.
October 23, 2025 at 11:13 AM
lifeonthewedge.bsky.social
Icecream🍦builds upon amazing packages such as cryo-CARE, IsoNet and DeepDeWedge in particular. By introducing regularization by the equivariance loss to exploit natural symmetries in the data and some technical improvements, Icecream🍨 achieves superior denoising and MW filling 🤩
October 23, 2025 at 11:13 AM
lifeonthewedge.bsky.social
real carboxysome with ribos, thylakoids and a mysterious triangle to scale 😉

(from @sofie-dot-rec.bsky.social)
Slice of a cryo-ET volume showing a carboxysome, thylakoid membranes, ribosomes and a mysterious triangular structure.
September 24, 2025 at 9:17 PM
lifeonthewedge.bsky.social
I never expected to write this line of code
September 18, 2025 at 10:30 PM
lifeonthewedge.bsky.social
Off to a good start, a giant #Calder just outside the station

#Grenoble
June 25, 2025 at 5:40 PM
lifeonthewedge.bsky.social
Dear #Basel friends, on May 10th @apbstudio.bsky.social is once more organizing the #WorldCollageDay celebration ✂️🤩

Join us for a relaxing and fun afternoon of #collage making at the Foyer Public of the Theater Basel!
May 2, 2025 at 3:16 PM
lifeonthewedge.bsky.social
Clearly this TIE fighter
April 23, 2025 at 12:47 PM
lifeonthewedge.bsky.social
We have updated our #MemBrain v2 preprint with a lot more details about the MemBrain-pick and MemBrain-stats modules, as well as some application examples!

Stay tuned for the upcoming thread by lead author @lorenzlamm.bsky.social! 🧠🧵

#CryoET #TeamTomo
www.biorxiv.org/content/10.1...
Figure 4. MemBrain v2 end-to-end workflow detects periodic phycobilisome organization. A: Raw tomogram slice of EMD-31244. B: Out-of-the-box MemBrain-seg segmentation (light blue). C: A single membrane instance can be visualized in Surforama and manually annotated with GT phycobilisome positions (magenta). D: MemBrain-pick localizes particles (trained with data from C) on all membranes in the tomogram. E: MemBrain-stats computes Ripley’s O statistic using the positions from D with a bin size of 5nm. The distance between peaks (35 nm) was measured to estimate chain unit spacings.
April 23, 2025 at 8:47 AM
lifeonthewedge.bsky.social
First, we had accidentally uploaded cryo-CARE tomograms that were calculated using an outdated version of the tilt series alignments. In most cases the differences were small, but noticeable. This concerns all tomograms numbered <= 712, or 464 tomograms
(bad tomos were not uploaded, hence the skips)
Slices through a tomogram of a Chlamydomonas pyrenoid, before and after the alignment update.
February 28, 2025 at 4:35 PM
lifeonthewedge.bsky.social
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
Rare cellular events observed in the cryo-ET dataset. Slices through tomograms (left) with corresponding 3D segmentation (middle and right). Right panels show enlarged views of the boxed regions in the middle panels. A) Mitochondrion at the plasma membrane, tethered to microtubules by thin filaments of unknown identity. Segmented classes: nuclear envelope (light blue), nuclear pore complex (dark blue), 80S ribosomes (orange), mitochondrial membranes (dark red), ATP synthase (royal blue), plasma membranes (grey), microtubules (pink), filaments (yellow), endoplasmic reticulum (purple). Zoomed-in panel shows thin filaments running between microtubules and the mitochondrion at the plasma membrane. Note that this tomogram contains two closely appressed cells, and thus, two plasma membranes with cell walls between. B) Mitochondrial fission event with ER membrane interactions. Segmented classes: mitochondrial membranes (dark red), ATP synthase (royal blue), 80S ribosomes (orange), thylakoid membranes (green), PSII (bright yellow), cell wall (grey), ER (purple), fission site containing filamentous structures perpendicular to the mitochondrial long axis (pale yellow). C) Ciliary transition zone between basal body and axoneme, including assembling IFT train and stellate structure77. Segmented classes: microtubule doublets (light blue), central microtubule pair (light green), stellate structure (pale red), IFT train (yellow). D) Pyrenoid tubule extending from the thylakoids into the phase-separated Rubisco matrix of the pyrenoid. Minitubules originate from thylakoid membranes82. Segmented classes: thylakoid membranes (dark green), PSII (yellow), pyrenoid tubule (lime green), Rubisco (lavender blue), minitubules (orange). Scale bars in A-D: 100 nm. Related to Fig. 2C-H.
February 28, 2025 at 4:35 PM