CryoSPARC Live™ is a platform for real-time cryo-EM data quality assessment and decision making during a collection.
Now generally available
First launched in May 2019 and beta tested at dozens of facilities globally, cryoSPARC Live™ enables go/no-go decision making about cryo-EM samples on the basis of real-time 2D and 3D feedback, within a few minutes to hours of starting a collection.
CryoSPARC Live features a novel processing pipeline and interface, providing a new level of insight into data:
"CryoSPARC Live enables the Pacific Northwest Cryo-EM Center to keep up with data coming from all 5 of our microscopes, a data volume that has at times exceeded 15TB (30,000+ images) per day. We can monitor not only standard image pre-processing metrics, but also directly observe improvements to 3D maps concurrent with data collection! In many cases we’ve stopped data collection with a 2.2-3.5Å map already in hand. We can also quickly identify pathologies such as poor orientational distributions, or tune imaging conditions to improve alignment of difficult particles."
In our facility, cryoSPARC Live has completely revolutionised the way we collect and process cryoEM data. Initially, we commissioned cryoSPARC Live with the primary goal of feedback on micrograph quality through on-the-fly motion correction and CTF estimation. But it has turned out to be so much more than we hoped for. We now use it for all initial processing of data coming through our facility. Our latest GPU workstation was specifically specced out for rapid cryoSPARC processing as it has become our primary in-house processing tool. Some of the aspects we love about cryoSPARC Live include: the GUI is intuitive, easy to use, and easy to learn for new users; processing is extremely fast; parameter changes are propagated throughout the workflow in a streaming fashion; easy linkages with ‘regular’ cryoSPARC make continued processing simple; picking tools are easy to use and work for almost all targets, and micrograph curation is powerful and easy to apply. CryoSPARC has become such an essential part of our data collection and analysis workflow; we could not imagine working without it. Highly valuable microscope time is now used much more efficiently and our microscope users are very satisfied.
CryoSPARC live may literally make your jaw drop. The speed of processing combined with the capability to make adjustments in real time are remarkable. It allows you to make go/no go decisions for each experiment using 2D and 3D results generated almost as fast as the images can be collected. Perhaps most impressive is the ability to go back and change almost any parameter on the fly, and it will immediately reprocess the images from that step, and key metrics such as motion and CTF fit can be examined in interactive plots where ranges can be set and immediately applied for image curation. Together these features take a large step toward the future in reducing both the time and resources that are needed to achieve a successful outcome for each data collection.
My group and I have been using cryoSPARC Live beta for a little over a year with great successes. We currently only run cryoSPARC Live for our in house projects and it has been of great help. It is easy to set up, very easy to use and very fast. There is no need to create scripts or any slightly complicated task. On most projects with very limited human interaction and no knowledge of the target of interest we can reach high resolution overnight before the run on the microscope is finished. The cryoSPARC-live features allow us to monitor the quality of the acquisition and make modifications in real time if necessary, whether it is a sample problem (e.g. ice thickness) or an issue with the alignment of the microscope. We are looking forward to extend the use to the core facility users allowing them to get real time feedback on their runs.
CryoSPARC Live is a wonderful tool that not only gets researchers excited about their cryoEM experiments but lets microscope operators know they are acquiring high-quality processable data. With on-the-fly feedback users and staff are able to engage with each other to identify bottlenecks and modify data collection strategies in real-time to conduct optimized experiments for a sample. 3D feedback is critical because it ensures we are able to collect a full dataset of their macromolecule of interest, thereby allowing our users to accelerate their biomedical research.
Having used CryoSPARC Live at both New York Structural Biology Center (USA) and The Hospital for Sick Children (Canada), it has become an invaluable tool in real time assessment of samples for a frequent user like me. By having the movie frames aligned, CTF estimated, particles picked, 2D classification and ab initio done on the fly allows me to quickly judge which grid/sample is worth collecting on. As all the statistics can also be neatly presented as an overview, it is straightforward too to pick out trends and exceptions in the data: For instance I have noticed cases where a bunch of micrographs had poor estimated resolution, only to pinpoint the problem to a single grid square, allowing me to avoid similar grid squares subsequently. The final big advantage of CryoSPARC Live is that the resulting data can easily be passed onto the conventional CryoSPARC pipeline for further processing – saving both time and energy!