Skip to content

CHEATSHEET.md

Latest commit

 

History

History
58 lines (40 loc) · 882 Bytes

CHEATSHEET.md

File metadata and controls

58 lines (40 loc) · 882 Bytes
Raw

📝 AreTomo Batch – Quick Cheat Sheet

1. Install

git clone https://github.com/your-repo/aretomo-batch.git
cd aretomo-batch
pip install tqdm

2. Prepare data

Each tilt-series needs:

TS_01/TS_01.st
TS_01/TS_01.rawtlt

3. Run alignment

aretomo_batch.py raw_data/ aretomo_align/ \
                 -j 8 -g 0,1 \
                 --align-z 1000
  • -j = concurrent jobs
  • -g = GPU list
  • --align-z = sample thickness (px)

Logs → aretomo_align/logs/ Summary → aretomo_align/processing_summary.json

4. Reorganise for Warp

aretomo_export_for_warp.py aretomo_align/

Creates Warp-ready structure:

aretomo_align/
├── Position_01/   # contains .mrc, .aln, logs/
├── Position_02/
└── imod/          # IMOD files preserved

✨ Done → Import directly in Warp!