CryoNet: Cryo-EM 3D Reconstruction Model

CryoNet is a 540M parameter cryo-EM reconstruction model. Given a set of single-particle micrographs, it produces a 3D density map at near-atomic resolution while using roughly 10x fewer particles than conventional pipelines.

At a glance

Field	Value
Category	Imaging
Parameters	540M
Version	v1.4
Endpoint	`POST /v1/models/cryonet/predict`
Output	3D density map plus FSC and symmetry report

Install

pip install bunker-fold

See Installation for full setup, including uv and poetry.

When to use

Reconstruct a 3D map from a small particle set.
Get a fast preliminary map during a data collection session.
Resolve symmetry ambiguities before running a full refinement.

Example

curl -X POST https://api.bunkerbio.com/v1/models/cryonet/predict \
  -H "Authorization: Bearer $BUNKER_API_KEY" \
  -H "Content-Type: application/json" \
  -d '{
    "particles": 12400,
    "pixel_size": 1.06,
    "voltage": 300,
    "defocus_range": [1.2, 3.0],
    "input_url": "s3://my-bucket/particles.star"
  }'

import requests, os

r = requests.post(
    "https://api.bunkerbio.com/v1/models/cryonet/predict",
    headers={"Authorization": f"Bearer {os.environ['BUNKER_API_KEY']}"},
    json={
        "particles": 12400,
        "pixel_size": 1.06,
        "voltage": 300,
        "defocus_range": [1.2, 3.0],
        "input_url": "s3://my-bucket/particles.star",
    },
)
print(r.json())

Response

{
  "resolution_angstrom": 2.8,
  "fsc_threshold": 0.143,
  "symmetry": "C1",
  "map_size": [256, 256, 256],
  "processing_minutes": 14,
  "particles_used": 11820,
  "map_url": "https://cdn.bunkerbio.com/maps/xyz789.mrc"
}

Parameters

string

required

Signed URL or S3 path to a particle STAR file or a directory of micrographs.

integer

required

Number of particles in the input set.

number

required

Pixel size in angstroms.

integer

Accelerating voltage in kV. Typical values are 200 or 300.

number[]

Two-element array [min, max] in micrometers.

string

Optional symmetry hint (C1, C2, D2, I, etc.). Defaults to automatic detection.

Response fields

number

Reconstructed resolution in angstroms at the reported FSC threshold.

string

Detected or applied symmetry group.

integer

Number of particles that contributed to the final map after outlier rejection.

string

Signed URL to the reconstructed density map in MRC format. Valid for 24 hours.

Get Started

Models

API Reference

Installation

CryoNet: Cryo-EM 3D Reconstruction Model

At a glance

Install

When to use

Example

Parameters

Response fields