All algorithms

Decoy classification

Stage

2

of 8

Included on all plans

Automated Junk Generator

Decoy maps generated from your reference, so junk particles sort themselves into classes you can throw away.

From a reference

Decoys made from the map you already have

Automatic

No decoy classes to build by hand

What it does

A particle stack always contains junk: picks on noise, aggregates, damaged particles. In 3D classification, junk has to go somewhere, and without a better option it spreads across the real classes.

A common remedy is to give it somewhere better to go: decoy classes that resemble nothing real, which junk particles match more readily than they match the true structure. The Automated Junk Generator makes those decoys for you from a reference map, so junk particles sort themselves out.

How it works

Starting from your reference map, the job generates decoy maps which you can provide as additional references in 3D classification. Real particles still align best to the target reference. Particles that are not really the target fall into the decoys, and are discarded.

Doing this automatically matters because good decoys are tedious to build by hand, and in CryoCloud decoys can already be kept with each target alongside its primary map and masks.

Orientation coverage clustered at one pole, and its effect on a density map

Decoy maps generated from real data. They carry no real structural information, and act as sinks for junk particles.

Where it sits

An optional step before decoy-based classification.

At a glance

Stage

Decoy classification

Runs

Automatically, during classification

Hardware

Cloud compute

Inputs

A reference map and a particle stack

Outputs

Decoy classes and a cleaner stack

Particles that land in decoys are removed with them.

Replaces

Availability

Included

Let junk sort itself out instead of picking it out by eye.

Frequently Asked Questions

If it's not covered here, please reach out to us.
…or start your free trial and see for yourself.

Is there a free trial?

Yes — when you sign up, you'll get instant access to a 30-day free trial with full access to the CryoCloud web application. You'll receive 20 hours of compute time and 2 TB of storage. No setup or infrastructure needed. After the trial, you can upgrade to a paid subscription or contact us for custom plans — no interruption to your data.

How can I start using CryoCloud?

Either go directly to out signup page or simply send us an email to hi@cryocloud.io so we can invite you to our application. You can find more information on how to get started here.

Do I need to install anything?

No - you really just need a (simple) computer, internet access and an internet browser. We took care of everything else. Read more on it here

How does your risk-free trial work?

If you are unsatisfied, you can cancel your plan within 30 days and we will refund you at 100%. You can deactivate the subscription from your account settings.

Frequently Asked Questions

If it's not covered here, please reach out to us.
…or start your free trial and see for yourself.

Is there a free trial?

Yes — when you sign up, you'll get instant access to a 30-day free trial with full access to the CryoCloud web application. You'll receive 20 hours of compute time and 2 TB of storage. No setup or infrastructure needed. After the trial, you can upgrade to a paid subscription or contact us for custom plans — no interruption to your data.

How can I start using CryoCloud?

Either go directly to out signup page or simply send us an email to hi@cryocloud.io so we can invite you to our application. You can find more information on how to get started here.

Do I need to install anything?

No - you really just need a (simple) computer, internet access and an internet browser. We took care of everything else. Read more on it here

How does your risk-free trial work?

If you are unsatisfied, you can cancel your plan within 30 days and we will refund you at 100%. You can deactivate the subscription from your account settings.

Frequently Asked Questions

If it's not covered here, please reach out to us.
…or start your free trial and see for yourself.

Is there a free trial?

Yes — when you sign up, you'll get instant access to a 30-day free trial with full access to the CryoCloud web application. You'll receive 20 hours of compute time and 2 TB of storage. No setup or infrastructure needed. After the trial, you can upgrade to a paid subscription or contact us for custom plans — no interruption to your data.

How can I start using CryoCloud?

Either go directly to out signup page or simply send us an email to hi@cryocloud.io so we can invite you to our application. You can find more information on how to get started here.

Do I need to install anything?

No - you really just need a (simple) computer, internet access and an internet browser. We took care of everything else. Read more on it here

How does your risk-free trial work?

If you are unsatisfied, you can cancel your plan within 30 days and we will refund you at 100%. You can deactivate the subscription from your account settings.

Ready to skip the queue?
Start analyzing your cryo-EM data today.

We would love hear about your cryo-EM goals and discuss how we can accelerate them.

  • No infrastructure needed

  • Streamlined onboarding & legal support

  • Highest security

Ready to skip the queue?
Start analyzing your cryo-EM data today.

We would love hear about your cryo-EM goals and discuss how we can accelerate them.

  • No infrastructure needed

  • Streamlined onboarding & legal support

  • Highest security

Ready to skip the queue?
Start analyzing your cryo-EM data today.

We would love hear about your cryo-EM goals and discuss how we can accelerate them.

  • No infrastructure needed

  • Streamlined onboarding & legal support

  • Highest security

Accelerate scientific discovery with our cloud-native cryo-EM platform, from data collection to high-resolution structure determination.

Subscribe to our newsletter

© 2021-2026 CryoCloud B.V. All rights reserved.

Accelerate scientific discovery with our cloud-native cryo-EM platform, from data collection to high-resolution structure determination.

Subscribe to our newsletter

© 2021-2026 CryoCloud B.V. All rights reserved.

Accelerate scientific discovery with our cloud-native cryo-EM platform, from data collection to high-resolution structure determination.

Subscribe to our newsletter

© 2021-2026 CryoCloud B.V. All rights reserved.