iiinova — where your digital self keeps evolving

simon-alkema.bsky.social @simon-alkema.bsky.social · 17/09/2026

It's a single Python script, easy for biologists (and AI) to adapt to your own pipeline. Built in the Mattei group (@simonemattei.bsky.social ) at @embl.org Heidelberg with help from @nastiaincryo.bsky.social, Euan Pyle and @hvdrosa.bsky.social. Feedback and issues are very welcome!

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simon-alkema.bsky.social @simon-alkema.bsky.social · 17/09/2026

What it does: • XY/XZ/YZ viewer with synced zoom and pan • Flags that can double as counters • Ruler for quick size checks • Autosaves, so you can stop and resume anytime • A link command to collect e.g. all good tomograms with mitochondria for processing doi.org/10.5281/zeno...

doi.org

TOMATO: TOMogram Annotation TOol

TOMATO is a lightweight Python GUI for inventorying the contents of cryo-ET tomograms. It records one row per tomogram with the structures present, optional counts, a quality grade and a comment, and includes an orthogonal XYZ viewer. A link command creates symlinks to tomograms matching chosen annotations for downstream processing.

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simon-alkema.bsky.social @simon-alkema.bsky.social · 17/09/2026

Releasing TOMATO, the TOMogram Annotation TOol! A lightweight Python GUI for going through hundreds of cryo-ET tomograms. Flag what's in each one, grade its quality, and end up with a table you can filter and act on. github.com/alkemasimon/...

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