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Installation Guide

Requirements

Saber runs on Python 3.10 and above on Linux or Windows with CUDA12.

Quick Installation

Saber is available on PyPI and can be installed using pip:

pip install saber-em

⚠️ Note By default, the GUI is not included in the base installation. To enable the graphical interface for manual annotation, install with: 

pip install saber-em[gui]

Development Installation

If you want to contribute to saber or need the latest development version, you can install from source:

git clone https://github.com/chanzuckerberg/saber.git
cd saber
pip install -e .

Verification

To verify your installation, run:

saber

You should see the following output:

 SABER ⚔️ -- Segment Anything Based Expert             
 Recognition.                                                
╭─ Options ──────────────────────────────────────────╮
│ --help  -h  Show this message and exit.            │
╰────────────────────────────────────────────────────╯
╭─ Commands ─────────────────────────────────────────╮
│ analysis    Post-processing analysis after         │
│             segmentation.                          │
│ classifier  Routines for training and evaluating   │
│             classifiers.                           │
│ gui         Saber GUI for annotating SAM2          │
│             segmentations with custom classes.     │
│ save        Save organelle coordinates and         │
│             statistics (size-distribution) from    │
│             segmentations.                         │
│ segment     Segment Tomograms and Micrographs with │
│             SABER.                                 │
│ web         SABER Annotation GUI Web Server        │
╰────────────────────────────────────────────────────╯

Next Steps