3. STAR

The partinet star command is the final step in your particle picking pipeline. It converts the particle coordinates detected in the previous stage into a standardized STAR file format that can be used with downstream cryo-EM processing software like RELION, cryoSPARC, or other reconstruction programs.

Quick Start

Local Installation

partinet star \
    --labels /data/partinet_picking/exp/labels \
    --images /data/partinet_picking/denoised \
    --output /data/partinet_picking/output.star \
    --conf 0.1

Apptainer/Singularity

apptainer exec --nv --no-home \
    -B /data oras://ghcr.io/wehi-researchcomputing/partinet:main-singularity partinet star \
    --labels /data/partinet_picking/exp/labels \
    --images /data/partinet_picking/denoised \
    --output /data/partinet_picking/output.star \
    --conf 0.1

Docker

docker run --gpus all -v /data:/data \
    ghcr.io/wehi-researchcomputing/partinet:main partinet star \
    --labels /data/partinet_picking/exp/labels \
    --images /data/partinet_picking/denoised \
    --output /data/partinet_picking/output.star \
    --conf 0.1

Parameters

Parameter	Type	Required	Description
--labels	Path	Yes	Directory containing the particle coordinate files (.txt format) from the detection stage
--images	Path	Yes	Directory containing the denoised micrographs corresponding to the labels
--output	Path	Yes	Output path for the generated STAR file
--conf	Float	Yes	Confidence threshold for filtering particle coordinates (0.0-1.0)

Input Requirements

At this stage of the pipeline, your directory structure should look like:

partinet_picking/
├── motion_corrected/          # 📁 Your input micrographs
│   ├── micrograph1.mrc
│   ├── micrograph2.mrc
│   └── ...
├── denoised/                  # 🧹 Created by denoise stage
│   ├── micrograph1.mrc
│   ├── micrograph2.mrc
│   └── ...
├── exp/                       # 🎯 Created by detect stage
│   ├── labels/               # 📋 Detection coordinates
│   │   ├── micrograph1.txt
│   │   ├── micrograph2.txt
│   │   └── ...
│   ├── micrograph1.mrc       # 🖼️ Micrographs with detections drawn
│   ├── micrograph2.mrc
│   └── ...
└── partinet_detect.log
└── partinet_denoise.log

Confidence Threshold

The --conf parameter controls the quality filtering of detected particles:

• Typical range: 0.1-0.3 for most datasets

Choose your confidence threshold based on:

• Dataset quality and signal-to-noise ratio
• Downstream processing requirements
• Balance between particle quantity and quality

Output

The command generates a STAR file containing:

• Particle coordinates (X, Y positions)
• Corresponding micrograph paths

Next Steps

After generating your STAR file, you can:

• Import it into RELION/CryoSPARC for 2D classification and 3D reconstruction
• Perform additional particle filtering or sorting based on your specific needs

warning

PartiNet Denoise flips micrographs in the y-axis due to matrix transpose operations. If you denoised micrographs in PartiNet ensure that when you import and extract particle coordinates that you toggle Flip in y in CryoSPARC or similar in RELION prior to particle extraction.