Inside The Hive: A Modular Architecture For Future-proof Microscopy

NewsMedical speaks to Bettina Trauernicht and Lord Hess astatine Bruker astir really nan ACQUIFER HIVE strategy is transforming microscopy-based investigation by tackling nan increasing situation of large image information management.

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What situation does nan HIVE strategy purpose to lick successful microscopy-based research?

The Aquifer HIVE has been developed by an interdisciplinary squad of engineers, biologists, microscopists, physicists, and IT experts pinch galore years’ acquisition successful large information management. At its core, HIVE is simply a solution for handling ample image data, presently deployed successful complete 100 imaging facilities

sCMOS detectors are continually improving, and it is imaginable to get a batch of accusation from them, but this has led to a monolithic deluge of large image information that must beryllium processed.

For example, a azygous FISH signaling could characteristic 5 tiles pinch 340 slices each, each portion recorded successful 2 colors. All of these tiles could beryllium recorded six times successful 1 hr complete a play of 16 hours. At nan extremity of this process, we could beryllium dealing pinch astir 2.5 terabytes of image data.

Other experimental applications activity pinch moreover much image data. For example, an research looking astatine nan improvement of a Drosophila consequence alert pinch Bruker's Luxendo ray expanse exertion could grounds 21,600 clip points from some sides. This highly optimized strategy records 100 frames per second, and each framework has a record size of 8 megabytes. This research would consequence successful a information group that is 17 terabytes successful size.

With information volumes for illustration these becoming progressively common, nan HIVE strategy is designed to efficiently tackle nan awesome bottleneck successful microscopy workflows: handling and transferring monolithic image datasets.

Image Credit: MAXIMUM ART/Shutterstock.com

How does nan HIVE strategy minimize information transportation delays and microscope downtime?

A emblematic processing script successful either a multi-microscope situation aliases a single-microscope situation originates pinch nan microscope itself.

The microscope starts to get data, which is stored connected nan computing portion that controls nan microscope. Before analyzing this data, we could typically transcript it to an soul server and past onto a processing workstation capable to analyse it. HDDs aliases SSDs whitethorn besides beryllium utilized to move nan information around, copying information onto transportable devices and past onto workstations from there.

There are emblematic limitations successful these processing scenarios. First of all, depending connected nan web infrastructure, nan transportation of nan information itself could return a agelong time. Microscopes must often stay idle while copying this data, because copying information and acquiring information astatine nan aforesaid clip is not ever possible. This decreases nan uptime of nan microscope.

Using transportable SSDs aliases HDDs introduces further risks, including imaginable information vulnerabilities aliases strategy instability.

A emblematic 1 gigabit web transfers information astatine astir 100 megabytes per second, which is comparatively slow for ample datasets. For example, copying nan 2.5-terabyte dataset mentioned earlier would return astir 7.3 hours per step, first from nan microscope power portion to an soul server, and past to a processing workstation.

Copying nan 17-terabyte Drosophila dataset successful 2 steps would return astir 49.5 hours per transfer.

An SSD would return astir 3 hours to move nan 2.5 terabytes of information from nan power portion of nan instrumentality to nan strategy for analyzing, but nan 17-terabyte information group would airs a situation because it is difficult to find SSDs pinch information transportation rates of 500 megabytes per second.

These issues tin besides stem from aggregate devices. For example, wide section confocal aliases spinning disc confocal systems are producing information successful parallel, resulting successful truthful overmuch information that it tin clang a 10-gigabit network.

HIVE solves these issues successful large image information handling and microscopy by combining networking, storage, and computing. Data streams are taken from nan microscopes and live-streamed onto nan HIVE COMPUTE level and into nan HIVE DATA module. Our accuracy centers astir not moving nan information erstwhile it has been acquired. Instead, we move nan personification to nan data.

Four HIVE modules are available. The HIVE NET module is utilized for entree and communication, and nan HIVE DATA module is nan retention abstraction for microscopy information coming from high-content screening, omics data, sequencing data, and more. The HIVE CORE portion is capable to supply a multi-user login for information processing pinch a wide scope of package solutions available, and nan HIVE GPU module is utilized for visualization and analysis.

Can you explicate nan usability of nan HIVE NET module successful nan strategy architecture?

The HIVE NET module is nan internode for nan microscope. This module features HIVE Switch, a multi-plug for microscopes that tin plug into much than 21 devices.

A DHCP router strategy and firewall thief users make a unafraid subnetwork for microscopy, while an uninterruptible powerfulness proviso (UPS) wrong nan HIVE NET helps keep nan HIVE moving successful nan lawsuit of electrical fluctuations aliases loss. This UPS will besides safely unopen down nan strategy successful nan arena of a prolonged powerfulness outage.

It was important that we tested and approved nan strategy to guarantee its compatibility pinch a wide scope of different microscopes and hardware vendors. This allows america to guarantee that nan HIVE COMPUTE level is disposable to watercourse nan information from each a user’s devices.

What makes nan HIVE DATA module suitable for large-scale technological environments?

The HIVE DATA module is disposable successful aggregate sizes, ranging from 52 terabytes to 238 terabytes of usable space. Because it is simply a modular system, we besides person nan action to link plug-and-play extensions of nan first information module pinch different information modules, upgrading this information measurement up to a one-petabyte solution.

This module uses RAID 6 exertion to guarantee information safety. This intends nan HIVE DATA module combines 15 difficult disk drives into 1 volume, and moreover if 2 difficult drives fail, nan information is still safe. The module besides offers a accelerated information transportation complaint of astatine slightest 3 gigabytes per second.

How does nan HIVE CORE module support parallel, multi-user processing?

The HIVE CORE module is simply a multi-user processing level moving connected Windows Server 2022. It includes everything you request for processing, including a CPU, RAM, NVMe, SSDs, and a 10-terabyte SSD RAID 5 strategy for information storage.

The HIVE CORE portion is tested pinch package from a scope of vendors, truthful we tin beryllium judge that a user’s package will tally connected nan system.

It tin besides beryllium adapted according to personification requirements, accommodating nan number of group moving successful parallel successful a facility, lab, aliases different technological environment.

What types of precocious processing tasks is nan HIVE GPU module optimized for?

Different package needs different hardware to tally smoothly, truthful nan HIVE CORE tin beryllium extended pinch nan HIVE GPU module for GPU-accelerated processing. This module tin accommodate up to 4 dual-slot GPUs successful 1 container aliases up to 8 single-slot GPUs.

At nan moment, we are utilizing RTX Ada Generation graphics cards because nan HIVE GPU module is designed to supply nan GPU-accelerated processing powerfulness needed for applications for illustration 3D denoising, deconvolution, aliases AI applications.

How does nan HIVE Dashboard heighten personification and strategy management?

Our full squad is focused connected ensuring that nan HIVE strategy is arsenic easy to usage arsenic possible. The HIVE Dashboard is designed to remotely show nan wellness of nan HIVE system.

For example, if a difficult disk thrust breaks down, nan HIVE Dashboard app sounds an siren and provides a ocular cue, on pinch accusation connected nan faulty hardware needing to beryllium replaced. The Dashboard tin besides show LAN health, instrumentality temperature, web stability, and UPS load.

It is important to mention that users do not request to beryllium logged into nan HIVE Dashboard to person these alerts, because nan HIVE besides communicates pinch users by email. For example, an administrator will get an email notification if thing happens that requires an alert to beryllium issued.

Another important characteristic of nan HIVE Dashboard is that it indicates if location are caller strategy updates. From wrong nan system, you tin besides interaction Bruker for work and support.

User guidance successful nan HIVE Dashboard allows users to beryllium assigned to nan HIVE, pinch personification credentials and passwords group from wrong nan system. The caller personification will past get an email notification pinch accusation connected really to log connected to nan strategy and really to alteration nan password. Users tin besides beryllium assigned different permissions, for example, pinch entree to nan Remote Desktop Protocol successful bid to entree nan HIVE via nan internet.

Users tin beryllium group up arsenic task leaders, and it is besides imaginable to clip limit personification access, for example, wherever a personification is collaborating connected a task for a constricted clip only aliases wrong circumstantial moving hours. Project information is stored successful shared folders, and we tin adhd circumstantial users to circumstantial folders connected a imperishable aliases time-limited basis.

All of these capabilities are mixed successful 1 package tool, truthful location is nary request to usage abstracted systems for wellness monitoring, personification management, and task management.

What makes nan HIVE strategy future-proof and scalable for evolving laboratory needs?

The Acquifer HIVE is an businesslike strategy pinch fantabulous information information capabilities. Maintaining nan cardinal retention of image information successful technological imaging environments avoids nan unnecessary plagiarism of information while offering users nonstop entree to nan information via nan HIVE CORE computing nodes.

The HIVE is an highly future-proof investment—the modular strategy grows successful statement pinch nan needs of nan lab. Users commencement pinch a mini HIVE and build up to a powerful workhorse strategy pinch a batch of storage. Each module comes successful its ain housing, which tin beryllium stacked connected apical of 1 different and connected via easy plug-and-play extensions.

The HIVE uses nan Windows Server 2022 operating system, which intends it is compatible pinch virtually each microscopy and microimaging processing software.

The strategy supports a server people record strategy capable to accommodate aggregate users and applications. For example, nan HIVE tin support virtualization pinch Hyper-V, aliases it tin tally an Omero server connected nan system. HIVE CORE units tin besides beryllium provided pinch Linux operating systems.

The HIVE is an independent and elastic solution that provides a fast, powerful standalone web that is independent of web postulation successful nan wider institution aliases organization. Its firewall, artillery pack, and router let users to protect nan HIVE from entree from nan outside, aliases it tin beryllium afloat integrated into existing IT infrastructures.

Setup is provided by Bruker’s trained technicians, who will instal and merge nan system, link immoderate microscopes aliases different devices, and cheque that everything useful smoothly earlier users statesman moving pinch nan system.

The HIVE strategy is useful for immoderate type of user, from nan halfway installation lead aliases nan azygous microscope personification to, for example, unit moving pinch elaborate technological information computing.

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About nan speakers

Dr. Bettina Trauernicht is simply a Product Sales Specialist astatine Bruker pinch a beardown attraction connected high-throughput imaging and handling large image information from microscopy. Dr. Trauernicht vanished her Ph.D. astatine nan Karlsruhe Institute of Technology / Germany wherever she first sewage successful interaction pinch image data-intensive projects successful life science. Prior to joining Bruker, she was progressive successful nan income of nan ACQUIFER Imaging Machine and HIVE, now integrated into nan Bruker Fluorescence Microscopy portfolio.

Lord Hess is nan caput of Research and Development for Bruker´s ACQUIFER HIVE. His years of successful activity astatine nan “CERN – DataGrid Project” / Switzerland person laid nan instauration for nan ACQUIFER HIVE to go 1 of nan astir celebrated solutions for ample amounts of information successful nan life sciences. Lord Hess brings his expertise into nan Data Management conception to Bruker

About Bruker Nano Surfaces and Metrology

Bruker Nano Surfaces and Metrology provides high-performance, specialized study and testing exertion for nan widest scope of investigation and accumulation applications.

Our wide portfolio of 2D and 3D aboveground profiler solutions proviso nan circumstantial accusation needed to reply R&D, QA/QC, and aboveground measurement questions pinch speed, accuracy, and ease. And our tribometers and mechanical testers present applicable information utilized to thief amended improvement of materials and tribological systems. Bruker’s industry-leading quantitative nanomechanical and nanotribological trial instruments are specifically designed to alteration caller frontiers successful nanoscale materials characterization, materials development, and process monitoring.

Bruker has been starring nan description of atomic unit microscope (AFM) capabilities since nan very beginning, and our systems are nan astir cited AFMs successful nan world. Our broad suite of AFMs enables scientists astir nan world to make discoveries and beforehand their knowing of materials and biologic systems.

With our nanoIR technology, Bruker is now besides nan recognized leader successful photothermal IR spectroscopy from nan nanoscale to nan sub-micron and macro scales. And, arsenic nan only AFM shaper pinch a state-of-the-art probes nanofabrication installation and worldwide, application-specific customer support, Bruker is uniquely positioned to supply nan equipment, guidance, and support for each your nanoscale investigation needs.

Bruker’s suite of fluorescence microscopy systems provides a afloat scope of solutions for life subject researchers. Our multiphoton imaging systems supply nan imaging depth, velocity and solution required for intravital imaging applications, and our confocal systems alteration compartment biologists to study usability and building utilizing live-cell imaging astatine speeds and durations antecedently not possible.

Bruker’s super-resolution microscopes are mounting caller standards pinch quantitative azygous molecule localization that allows for nan nonstop investigation of nan molecular positions and distribution of proteins wrong nan cellular environment. And our Luxendo light-sheet microscopes, are revolutionizing semipermanent studies successful developmental biology and investigation of move processes successful compartment civilization and mini animal models.

In summation to processing and manufacturing next-generation systems to thief our customers’ existent and early applications, Bruker is besides very progressive successful acquiring and partnering pinch innovative companies to proceed to grow our scope of enabling technologies and solutions. Recent additions to nan Bruker Nano Surfaces family see Alicona Imaging, Anasys Instruments, Hysitron, JPK Instruments, Luxendo, Inscopix, and Neurescence.

Whatever your measurement and study needs, immoderate your worldly aliases standard of investigation, Bruker has a specialized high-performance solution for you.