Interactive curation of particles picked in cryo-electron tomograms.
Template matching (or any picker) finds your particles, but it over-picks: thousands of hits, most of them junk. PickyMate turns cleaning that list from a one-by-one slog into a few rounds of bulk decisions. Every pick carries a foundation-model embedding (TomoTwin, CryoSIAM); as you confirm good particles and reject junk, PickyMate re-ranks everything else by similarity to your own decisions — live, while you work — so lookalikes of what you confirmed come to you and lookalikes of what you rejected sink away. The same works across a whole dataset: decisions made in the tomograms you have finished re-rank the ones you have not opened yet.
The moment that matters, live from the app — you confirm a few good particles, and one click reorders thousands of picks around them:
Everything can also be fixed by hand — three orthogonal slice views, click
to add or remove a pick, organize into sets, all saved as plain x y z
text files. But start from the template-matching list: only its picks carry
embeddings, so a particle picked by hand cannot take part in the ranking.
With conda (creates a pickymate environment with the pickymate command):
git clone https://github.com/Image-Analysis-Hub/PickyMate.git
cd PickyMate
conda env create -f environment.yml
conda activate pickymate
Into an environment you already have — editable from a clone, or straight from GitHub:
pip install -e . # from inside the clone; edits take effect immediately
pip install git+https://github.com/Image-Analysis-Hub/PickyMate.git
pickymate tomogram.mrc # one tomogram
pickymate --session session.csv # a whole dataset
docs/ — a short, searchable user guide:
- Getting Started — running, command-line options, the two windows.
- Picking and Tools — Pick, Eraser, Select, and the Recycle Bin / Confirmed workflow.
- The Particle List — the thumbnail gallery and sets.
- Ranking by Embedding Distance — the heart of the tool.
- Sessions and UMAP Maps — many tomograms at once, and selecting particles directly on the embedding map.
- Selection, Undo, and Saving
- Keyboard Shortcuts
- Files on Disk — every file PickyMate reads or writes, all plain text.