Whole Slide Imaging & Analysis

MBF Bioscience > Whole Slide Imaging & Analysis

What is Whole Slide Imaging?

Whole slide imaging, also known as virtual microscopy, refers to scanning a complete microscope slide and creating a single high-resolution digital file. This is commonly achieved by capturing many small high-resolution image tiles or strips and then montaging them to create a full image of a histological section. Whole slide imaging is changing the workflows of many laboratories. Specimens on glass slides can now be transformed into high-resolution digital files that can be efficiently stored, accessed, analyzed, and shared with scientists from across the web using slide management technologies like Biolucida

Key Benefits:

Advanced technology solutions for whole slide imaging allows:

Aspects of Whole Slide Imaging:


Whole Slide Imaging Technology Falls into Three Main Categories:


Easily Sharable Digital Images

The digital nature of whole slide images allows for microscopic specimens to be easily be shared with others. Unlike the actual specimens, whole slide images do not deteriorate over time like specimens on glass slides. Whole slide images contain complete histological sections and enable the viewer to zoom to see high levels of detail, e.g. individual cells and subcellular structures. Put in another way, whole slide images enable the examination of histological sections at magnifications that range from a “bird’s eye view” to the highest level of detail provided at the time of image acquisition.

Data Storage and File Formats


Whole slide imaging produces data sets that require careful plans for data storage, organization, and access. There are currently few solutions that meet this requirement. 


File formats used in whole slide imaging have evolved with little or no standardization across the industry. Many commercial whole slide imaging scanners have adopted proprietary file formats that are dependent on unique software solutions to read and analyze the files. Other standards, such as OME TIFF, are loose standards that have many variations, many of which are not efficient for viewing, analyzing or web streaming.

The JPEG2000 (JP2) file format is the most effective one for all aspects of whole slide imaging. JP2s include a streaming format, multi-resolution capabilities, and efficient data compression. Only the most advanced software uses JP2 files format effectively.  MBF Bioscience products enable the utilization of formats from all major microscope and scanner manufacturers to ensure that scientific workflows produce data that and be efficiently accessed, analyzed, and shared.


JPEG 20000 extended part-2 specifications (JPX) files are able to store multiple JP2 files and MBF Bioscience software uses them to create three-dimensional image sets. By combining many whole slide images of serial sections into a JPX file, users can create massive image data files of whole organ reconstructions that are highly compressed for data sharing a storage.

Fields Of Study

The transformative technology of whole slide imaging has had a dramatic impact on many fields of research, including:

  • Pathology
  • Connectomics
  • Genomics
  • Archival libraries
  • Proteomics
  • Neuroanatomy
  • Medical Education
  • Medical Research Publishing

Whole Slide Imaging: Acquisition

Acquisition of whole slide images is achieved using a combination of microscope-based hardware and software. 

Whole Slide Scanners

Whole slide image scanners are specialized devices that are dedicated to acquiring high resolution images of entire slides. There are a wide variety of these products currently on the market. These scanners are typically designed for a single mode of illumination, either brightfield or fluorescent microscopy. The primary distinguishing factors (in addition to cost) in these products include:

1. imaging modality (brightfield or fluorescence)
2. quality of the images
3. speed of acquisition
4. size of the glass slides that can be scanned
5. optical resolution
6. 2D or 3D imaging capabilities.
Secondary distinguishing factors include ease of use, reliability, and file format support.

Our Solutions for Whole Slide Image Acquisition


MBF Bioscience has partnered with Huron Digital Pathology to offer a line of brightfield slide scanners, TissueScope, that is available from MBF Bioscience which have been specially designed for neuroscience and other biomedical research applications. These scanners can create 2D and 3D whole slide images using a variety of glass slides ranging in size from standard 1”x3” (25mm x 75mm) to ultra large 6”x8” (150mm x 200mm).

Whole Slide Imaging: Analysis

The analysis of whole slide images is a field that is rapidly evolving. There are numerous quantitative measurements that can be performed on these images. Specialized software is often required, as the large size of the images requires software techniques designed to work with these images without requiring long wait time by users.


Types of quantitative analysis include:


    • measuring sizes of objects and regions,
    • counting objects such as cells, axon terminals, etc.
    • measuring lengths of objects such as dendrites, capillaries, etc.
    • measuring density objects, such as protein based biomarkers, etc.

There are two main categories of analysis techniques:

    • Image processing
    • Machine learning (including high-throughput and user-assisted Stereology.)

Our Solutions for Whole Slide Image Analysis


  • We have a variety of solutions to help you with your unique needs in Whole Slide Image analysis:


TissueMaker automatically generates a full resolution 3D reconstruction of any organ or tissue sample from serial sections so that you can easily view cells, structures, and lesions.


BrainMaker automatically creates full-resolution, 3D reconstructions of the entire brain (or any organ) from serial sections of whole slide images.


NeuroInfo enables whole brain experimentation for laboratories of every size. Neuronal populations and circuits are automatically characterized in brain volumes and overlain with brain region delineations in a standardized reference space to provide visual and quantitative anatomic context.


Neurolucida® 360

Neurolucida 360 is the premier tool used by neuroscientists to quickly and accurately reconstruct intricate neuronal structures that range in scale from complex, multicellular networks of neurons to sub-cellular dendritic spines and putative synapses.



Whole Slide Imaging: Management & Sharing

Software Solutions

Effective management of whole slide images is an important, but often-forgotten aspect of whole slide imaging.  Since the files are often very large and in non-standard file formats, specialized software is required to manage the files.  Typically, laboratories generate terabytes of image data and don’t have a good solution to categorize and view this data.  We designed Biolucida to solve this problem. After whole slide images are acquired, these images can be viewed, categorized and stored on either local networks or using cloud-storage. Whole slide images can be instantly shared with colleagues for collaboration in your lab, down the hall, or around the world.  Biolucida supports file formats from virtually all commercial whole slide scanners.

Archival Libraries


Digital libraries containing collections of important microscopic specimens are increasingly being used in medical research and education. Important uses for whole slide libraries and web resources include:  digital histology collections, brain atlases, connectivity maps, and gene databases. Biolucida is designed to manage large collections of on-line whole slide images. It includes special features for collections, tags and sophisticated searches.

Our Solution for Whole Slide Imaging: Management & Sharing


Biolucida is leading the big data revolution by providing scientists and medical educators a cost effective and powerful solution to the many challenges it presents.  Data sets that in the past have been too voluminous and complex for traditional systems, can now be easily managed with Biolucida.

Want Help Understanding Which Product is Right for Your Application?

At MBF, we’ve spent decades understanding the needs of researchers and their labs — and have a suite of products and solutions that have been specifically designed for the needs of today’s most important and advanced labs. Our commitment to you is to spend time with you discussing the needs of your lab — so that we can make sure the solutions we provide for you are exactly what you’ll need. It’s part of our commitment to supporting you — before, during, and after you’ve made your decision. We look forward to talking with you!