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Life Science

Accelerate your Life Science Research with Fixstars latest Technology

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Fixstars is a provider of software and hardware for research labs, medical professionals, and biotech businesses to answer biological questions. We are assisting researchers all around the world in producing real results from their biological data with our reliable and reproducible analysis procedures and well-annotated solutions.

The need for trusted, actionable evidence has never been greater

Establish evidence

Unlock insights from the industry's largest archive of linked, longitudinal real-world computing solutions


Improve your value story

Engage our engineering experts to architect computing systems for your bio research.


Turn theory into action

Leverage our extensive bioinformatics knowledge and great skills to create and implement custom apps across all areas to meet your requirements.

Our Services

Acceleration service for NoRMCorre

Scientists, artists, and engineers require massive parallel computational capability. Fixstars provides GPU-optimized virtual machines that take advantage of the capabilities of CUDA, Tensor, and RT cores to run complicated processing, deep learning, and ray tracing tasks.

NoRMCorre is an algorithm widely used among scientists, and most commonly used in calcium imaging for neuroscience. However, it is also one of the most time-consuming pipelines used for neuroanalysis. We port and optimize NoRMCorre to GPU, and our GPU version will run twice as fast as the original CPU version of NoRMCorre in a rigid mode data set. This service will improve the overall lead time.

You concentrate on your key talents, while we worry about the hardware that enables them. Fixstars GPU machines lower the entry barrier for complicated use cases like machine learning and AI.

Fixstars GPUs are NVIDIA A100, which are now regarded as among the best on the market. These GPUs support any use case connected with parallel processing, deep learning, or ray tracing thanks to CUDA, Tensor, and RT cores in each unit.

Is one GPU card insufficient for your anticipated workloads? It's not a problem. Fixstars GPU plans include up to four cards per instance, depending on the amount of horsepower required.


In-Situ Sequencing Acceleration

A highly multiplexed method for precisely finding numerous RNA molecules within cells and tissues at the same time.

The in-situ sequencing (ISS) facility offers spatially resolved gene expression data at the subcellular level for panels of genes.

  • Preservation of spatial information in a tissue context
  • Targeted approach, using padlock probing
  • Highly specific amplification tool, offering multiple levels of molecular specificity
  • Multiplexing, up to a few hundred transcripts per sample
  • Sensitivity, tunable
  • High throughput due to wide-field imaging

Our Process

We speed up the software used for in-situ sequencing by identifying bottlenecks and optimizing the computer code. Whether it's GPU clusters, high-speed data storage, or one of our other services, we'll employ whatever is best for your applications.

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Expansion Microscopy Studio

Overcoming Microscope Limitations


Expansion microscopy (ExM) is a method that physically magnifies tissues in an isotropic manner, allowing for super-resolution imaging using diffraction-limited microscopes and a huge field of view.

As a result, ExM is well-positioned to integrate molecular content and cellular morphology, with the spatial precision required to resolve individual biological building blocks as well as the scale and accessibility required to deploy over extended 3-D objects such as tissues and organs.

Learn More about ExM Studio icon

The Role of Imaging in the ExM Process

  1. Labeling
    Fluorophores are attached to biomolecules (in the post-expansion labeling method this step is performed at the end, after the expansion)
  2. Anchoring
    Molecular handles are covalently attached to biomolecules and/or labels. These cross-linkers enable the polymer matrix to exert tension on the biomolecules
  3. Gelation
    The polymer chain is broken down into its essential pieces to avoid injuring the cells (its building blocks). A monomer solution (sodium acrylate) and a highly penetrating hydrogel are applied to the specimen (sodium polyacrylate).
    Once within the cells, a chemical process occurs, and the monomers bind to form the appropriate polymer network
  4. Homogenization
    Enzymatic digestion or a heat and detergent treatment (denaturation/dissociation) is used to chemically disrupt the sample. The homogenization technique used is determined by the nature of the specimen and the molecules to be seen
  5. Expansion
    Water diffuses into the polyelectrolyte hydrogel by osmotic force when the specimen is immersed in it. The polymer will expand as a result of the water. The expansion isotropically pushes apart attached biomolecules, leaving large gaps between them. The extended specimen's spatial organization is intact, allowing nanoscale imaging with ordinary fluorescence microscopes.
  6. Image
    Image analysis
    The microscopes will capture images of the specimen, and those images will be uploaded to the image processing software. The two primary components of imaging for the ExM process are deconvolution and stitching. Deconvolution is a method used to reduce noise and sharpen the image. Stitching is a tool to stitch one sequence of a 2D image in 3D space, and create a whole 3D image data. Both processes are essential for ExM, but both are vastly time consuming, depending on the size and amount of images.
    This is where the Fixstars ExM Studio can accelerate the imaging process.

Why wait? Use the power of GPUs to accelerate your research!


ExM Studio

The ExM Studio is a software package for Expansion Microscopy. It accelerates the software for the two primary components of the imaging process: deconvolution and stitching.

GPU accelerated deconvolution

With the GPU acceleration you get the same high-quality results as before, but much faster! Using high-end NVIDIA GPU cards you achieve astonishing deconvolution results in seconds. The GPU mode also has the distinctive brick-splitting capability, allowing you to deconvolve very huge files on the GPU,with limited video -RAM. Furthermore, the algorithm can accurately compensate for spherical aberration in the event of a refractive index mismatch.

GPU acceleration runs a small piece of the application code that requires substantial computing time on the GPU, while the rest of the code runs on the CPU. Because the GPU is made up of hundreds or even thousands of distinct processing units (cores), it is incredibly efficient and quick at processing computationally intensive code.


GPU accelerated stitching

We offer a scalable hybrid CPU-GPU image stitching system that works with huge image sets at nearly interactive speeds. Both picture sizes and the number of CPU cores and GPU cards in a machine grow well with our method.

With this implementation, coarse-grain parallelism is utilized. The computation is organized into a pipeline architecture that utilizes both CPU and GPU resources and overlaps computation with data movement. The translation of each tile is estimated during the initial phase of deployment.

The method outperforms our optimized non-pipeline GPU implementation by almost 10 times and exhibits near-linear speedup with increasing CPU thread count and GPU count.

The tiles are joined together into a mosaic in the second stage using the calculated translations. However, because they create an overly restricted set of equations, these translations cannot be applied directly. By treating the system as a graph and gradually merging strongly-connected components, our method overcomes this constraint.

We gauge the strength of the connections using the cross-correlation values. By reducing uncertainty, this optimization improves stitching precision.

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Fixstars All-Flash NAS Solution

Validated Strong Performance and Functionality


All-Flash NAS is a fast, cost effective all-flash storage device for 3D microscopes. It stores, writes, and reads microscope data at I/O rates of 23-25Gbps for reads and 5Gbps for random writes (Lightsheet LiveScan needs a minimum of at least 2 Gbps for writing).

Microscope image reading & writing and I/O will be much faster and cost effective with this accelerated technology. Images can be transferred back and forth between microscope, software and storage systems at a fast rate.

Case Study


University of California, Los Angeles, Dr. Dong's Lab.

UCLA Dr. Dong's laboratory introduced a microscope all-flash NAS based on QNAP where 25Gbps connection is available between 3D microscopes and the AFA.

Fixstars tuned up the microscope all-flash NAS for Lightsheet workloads and it reaches 23Gbps reads and 5Gbps small file writes with the cost-efficient read-intensive SSD arrays. By our solution, they can enjoy full bandwidth for image reads in data analysis and enough random writes for Lightsheet's LiveScan workload.

Read the full case study

Our Process

Microscope scans the sample/specimen
Uploads sample to linked microscope computer (sequential/random writing)
Sample is stored in the All-Flash NAS 250 TB storage device at 23 Gbps for reads

Performance Advantages:

A faster read and write process results in faster I/O between microscopy samples and storage devices
Increases Gbps rate while remaining cost efficient in most cases, high Gbps rates will call for more expensive software devices
Maximizes bandwidth for image reading in data analysis and enough random writes for Lightsheet’s LiveScan workload
Optimizes bandwidth for image reading in data analysis and provides sufficient random writes for Lightsheet's LiveScan workload
Selects read-intensive SSDs. Typically, read-intensive SSDs have poor write performance, but they are less expensive than other types of SSDs. With our Read more
More than doubles the required amount of Gbps random write speed (2Gbps to 5Gbps)
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