Complimentary Science Software License

End User License Agreement

Scope of this Software License Agreement:

This is the SPHIRE-crYOLO Complimentary Science Software License Agreement, which applies to all software products available for download from the SPHIRE-crYOLO website(s), unless labeled as something other than complimentary.

The licensed Software / Product:

Short description of the software:

We present an automatic particle picking procedure for single particle electron cryomicroscopy (cryo-EM) called crYOLO, which is based on the well-known deep learning object detection system “You Only Look Once” (YOLO). We used three cryo-EM datasets from the EMPIAR databank to test crYOLO. After training crYOLO with not more than 2,500 particles per dataset, it selected the particles with high precision and accuracy. Irregularly-shaped particles are also well centered during selection and, in addition, the YOLO approach allows crYOLO to account for the context of the particle. Using standard NVIDIA GPUs, crYOLO picks up to 6 micrographs per seconds. The quality of crYOLO particle selection significantly speeds up processing and may even improve the achieved resolution. Furthermore, we showed that trained by multiple datasets is generalizes and picks previously unseen datasets.

For further description see the

The following components of the software are provided as source code or in compiled form:

  1. crYOLO software for training and automated particle selection

  2. Pretrained weights for the generalizing model

Intellectual Property:

All software available for download via the SPHIRE-crYOLO website(s) are copyright Max-Planck-Society e.V. (Institute of Molecular Physiology, Group Raunser, Thorsten Wagner) unless otherwise stated. Copyright law protects this software and any associated material. Max-Planck-Society e.V. retains title to and ownership in the copyright of the software program and the associated materials. This software is not provided as public domain software.

Complimentary Science Software License Rights:

The Software is licensed for non-commercial academic and research purposes only. All software products available for download from associated website(s), unless labeled otherwise, are provided royalty free. The software may be used as many times as you like until the contract is terminated. Licensor can terminate the contract at any time, in writing or Email. You must destroy your copy of the software after termination of this contract. You may not copy and distribute copies of this program, except for the reasons given in § 69d UrhG (Urhebergesetz). The copyright holder reserves the right to reclassify this software as another kind of software license product at any time (i.e. shareware, licensed royalty software, or public domain et al.). Doing so will modify the license agreement of previously distributed executables.

Use of the software is permitted for lawful scientific research purposes only. It is explicitly prohibited to use the SPHIRE-crYOLO software or parts of it, whether modified or not, for commercial purposes or operational use.

Code Immutability:

You may not modify, adapt, translate or create derivative works based upon the software. You will not reverse engineer, decompile, disassemble or otherwise attempt to discover the source code of the software except to the extent you may be expressly permitted by copyright holders or given in § 69d UrhG.

Warranty / Liability / Damages:

This program is provided “as is” and has not been fitted especially to Licensee’s purposes and comes with limited warranty and liability. Licensors do not provide any support for the software. Because this Software License Agreement qualifies as a donation, according to Section 521 of the German Civil Code (Bürgerliches Gesetzbuch – BGB) Licensors as donors are liable for intent and gross negligence only. If the Licensors fraudulently conceal a legal or material defect, they are obliged to compensate the Licensee for the resulting damage.

Licensors shall be liable for loss of data only up to the amount of typical recovery costs which would have arisen had proper and regular data backup measures been taken. For the avoidance of doubt Licensors shall be liable in accordance with the German Product Liability Act in the event of product liability. The foregoing applies also to Licensor’s legal representatives or assistants in performance. Any further liability shall be excluded.

Patent claims generated through the usage of the software cannot be directed towards the copyright holders.

Defects of the SPHIRE-crYOLO software must be notified in writing to the Licensors with a comprehensible description of the error symptoms. The notification of the defect should enable the reproduction of the error.

Third Party rights/components:

No third party components whatsoever are distributed with the SPHIRE-crYOLO software. Licensing of third party components is not part of this Software Licensing Agreement

Still, the Licensee is responsible for compliance with any respective third party license terms.

Technical Support:

Technical support may be provided via e-mail and/or website postings. While every effort is made to provide timely technical support no guarantees whatsoever are implied that technical support will be provided or that technical support, when provided, will be accurate. Software offered on this site is unsupported and supplied on an as-is basis unless you have obtained a specific maintenance contract agreement with the copyright holders.


This Complimentary Science Software License Agreement is effective while you use and continue to make use of these software products. If you do not agree with our Complimentary Science Software License Agreement you must not use our software products - this Complimentary Science Software License Agreement will then not apply to you. This Complimentary Science Software License Agreement is subject to change without notice. Any company names, logos, trademarks and product names mentioned or shown on associated website(s) or in software products may be copyrighted, trademarked or registered trademarked by their respective owners.

Final Provisions:

By using our software products you are automatically agreeing to and show that you have read and understood the terms and conditions contained within this Complimentary Science Software License. This Agreement shall be governed by the laws of the Federal Republic of Germany except for the UN Sales Convention.