FAQ

CryomaskR is available under two license types:

• Academic License — free of charge for non-commercial use by universities, research institutes, government laboratories, and not-for-profit organisations.
• Commercial License — required for any use by for-profit entities, or any use directed toward commercial advantage or monetary compensation. Commercial licenses are negotiated individually with MCALBYRNE LIMITED.

If you work for a for-profit organisation — including pharmaceutical companies, biotechnology firms, and contract research organisations — you require a Commercial License, regardless of whether the work is described as "research."

If you are at a university, government lab, or non-profit research institute and your use is purely for scholarly research or education, the Academic License applies.

If you are unsure, contact us before using the Software. We are happy to help clarify your situation.

See License Agreement, Article I (Definitions) and Article VII, Section 7.1.

Academic users may freely use, copy, and modify CryomaskR for:

• Scholarly research at universities, government labs, and non-profit institutes
• Teaching and academic coursework
• Personal education and training
• Publication of results in academic journals and presentations at scientific conferences

All copies must retain the copyright notice and license terms. Publications and presentations must cite CryomaskR appropriately.

Academic users may not, without a Commercial License:

• Use CryomaskR on behalf of a commercial entity — for example, running the software at the direction of a pharmaceutical or biotech company under a sponsored research agreement where that company directs the research objectives or retains commercial rights to the results
• Provide masks or other results generated by CryomaskR directly to a commercial entity
• Use CryomaskR to fulfil a contractual obligation to deliver specific commercial outcomes to a commercial sponsor
• Use CryomaskR in fee-for-service work where the service is provided to a commercial client
• Redistribute the Software to third parties outside of authorised distribution channels

See License Agreement, Article II, Section 2.2(d).

It depends on the nature of the funding arrangement:

• Unrestricted funding — where the funder does not direct research objectives or retain commercial rights to results — may qualify as Academic Use. For example, a general research grant from a pharma company that supports basic structural biology research, with no obligation to deliver results to the funder, would typically remain academic.
• Directed or restricted funding — where the commercial entity sets the research objectives, retains rights to results, or where there is a contractual obligation to deliver specific outcomes — constitutes Commercial Use and requires a Commercial License.

If you are unsure, contact us before using CryomaskR. We will help you determine the appropriate license at no cost or obligation.

See License Agreement, Article I, Section 1.2 (note on unrestricted funding) and Section 1.3.

Providing results generated by CryomaskR directly to a commercial entity requires a Commercial License. If your collaboration involves sharing CryomaskR outputs with a for-profit partner, that partner should hold a Commercial License, or the collaboration should be structured so that the commercial entity obtains its own license.

Contact us to discuss the best arrangement for your specific collaboration.

The suggested citation format is:

Calthorpe-Byrne, M.J. cryomaskR: [version]. Available at [repository URL]

Citation is a condition of the Academic License. Please include this in any publications or presentations that utilise the Software.

See License Agreement, Article II, Section 2.2(c).

Commercial licenses are negotiated directly with MCALBYRNE LIMITED. To begin the process, contact us at:

A Commercial License must be in place before the Software is downloaded, accessed, or used by a for-profit organisation.

Commercial licenses can be tailored to your organisation's requirements. Available terms include:

• Single-site or multi-site deployment — for organisations with one or more facilities
• Pipeline integration — for embedding CryomaskR into automated processing workflows
• Priority support and maintenance — including dedicated technical assistance and early access to updates

All terms are discussed during the licensing consultation.

See License Agreement, Article IV, Section 4.3.

Contact us to discuss evaluation options. We can arrange a demonstration or discuss a time-limited evaluation agreement that allows you to assess the Software before committing to a full license.

Contract research organisations require a Commercial License. CRO use falls under Commercial Use as defined in the License Agreement, regardless of whether the end client is academic or commercial. This includes fee-for-service cryoEM work and any use where the CRO is providing results to clients for compensation.

See License Agreement, Article I, Section 1.3(a) and 1.3(b).

CryomaskR is distributed exclusively through two authorised channels:

• Direct download from the official website at www.mcalbyrne.com/cryomaskr
• The SBGrid Consortium, under a separate Memorandum of Understanding

Downloads from any other source are not authorised.

See License Agreement, Article III, Section 3.1.

Yes. Users downloading CryomaskR directly must register with a valid name, institutional email address, and institution or organisation name. Registration constitutes acceptance of the License Agreement.

Registration data is processed in accordance with the MCALBYRNE LIMITED Privacy Policy.

See License Agreement, Article III, Sections 3.2 and 3.3.

No. The Software may not be redistributed or made available to third parties except through the authorised distribution channels listed above. Colleagues should download their own copy through the official website or SBGrid, so that each user registers and accepts the License Agreement individually.

CryomaskR currently supports macOS and Linux. A macOS DMG installer is available from the official website. Linux users can build from source via the GitHub repository.

If you see a message that "CryomaskR cannot be opened because it is from an unidentified developer," you can bypass macOS Gatekeeper using one of these methods:

Method 1: Right-click to open

1. Locate CryomaskR.app in Finder
2. Right-click (or Control-click) on the app
3. Select "Open" from the menu
4. Click "Open" in the dialog that appears

Method 2: Terminal command

1. Open Terminal
2. Navigate to where you downloaded CryomaskR
3. Run: xattr -cr CryomaskR.app
4. Double-click the app to open normally

Official Apple notarisation is in progress. Once complete, these steps will no longer be necessary.

CryomaskR integrates with standard cryoEM file formats and exports masks compatible with popular cryoEM software packages including RELION, cryoSPARC, and others. See the documentation included with the Software for a full list of supported formats.

For licensing enquiries, questions about permitted use, or any other matter not covered here:

This FAQ is published by MCALBYRNE LIMITED and may be updated from time to time. It supplements but does not replace the CryomaskR Software License Agreement (Ref: MCAL-LIC-CRYO-2025-001).