Core Facilities Solution


Core Facilities Solution Suite

 An Entire Suite of our Most Popular Software for Quantitative Image Analysis

MBF Bioscience now offers a unique, application-specific set of tools bundled into one comprehensive software suite. Fine-tune your research with a variety of our most popular software applications, which allow you to target the specific cellular structures you want and produce superior quantitative analysis. Using automatic and editing tools within your 3D reconstructions, you can navigate across a variety of pathways with precision, accuracy and speed to achieve your results. Moving easily across the cellular landscape with a high level of control, you’ll understand why this software is the industry leader with the most comprehensive set of built-in analyses, and is so much more than a generic image processing tool.

The new Core Facilities Solution Suite is now available as an annual subscription or a perpetual license  with special discounted pricing for core facilities.  The software licenses are provided on a single USB dongle and the annual subscription includes software upgrades and remote online technical support.

Benefits of the Core Facilities Solution Suite:

  • Increase the use of all your imaging instruments as our software can be used with image data from confocal, wide field, SIM, two-photon, light sheet and brightfield microscopes as well as whole slide scanners.
  • Import data easily with support for all of the most popular image file formats from Zeiss, Leica, Aperio, Olympus, Nikon, Hamamatsu, Huron and images from our new ClearScope light sheet microscope
  • Produce unbiased, quantifiable results with NIH-funded, award-winning scientific software
  • Receive full support from MBF’s technical support team, available to all users, with remote online technical support. Plus, all the software has built-in knowledge base
  • Save when you purchase all of the software as a suite rather than individual separate licenses
  • Generate a high impact with your research using MBF software tools that have helped researchers publish over 15,000 peer-reviewed papers in leading journals
  • Effortlessly move to any Windows 10 PC with the mobile license (dongle)
  • Access to 8 different software applications shown below

Customer Reviews

"MBF Bioscience is extremely responsive to the needs of scientists and is genuinely interested in helping all of us in science do the best job we can."
Sigrid Veasey, M.D.
University of Pennsylvania
"MBF provides excellent technical support and helps you to find the best technical tools for your research challenges on morphometry."
Wilma Van De Berg, Ph.D.
VU University Medical Center - Neuroscience Campus Amsterdam
"Our experience with the MBF equipment and especially the MBF people has been outstanding. I cannot speak any higher about their professionalism and attention for our needs."
Bogdan A. Stoica, M.D.
University of Maryland


Neurolucida 360 Studio:  Quickly and accurately reconstruct neurons in 3D and obtain reliable data about the specific neuronal structures such as axons, basal dendrites, apical dendrites, and axon-carrying dendrites while generating sophisticated analyses using the built-in analysis software.

Annual subscription includes one license for Neurolucida Explorer for morphometric analysis and the following features:

  • Full 3D environment for image visualization, rotation and zooming
  • Smart manual mode for targeted manual neuron tracing in 3D
  • User-guided mode for quick and easy semi-automatic neuron tracing in 3D
  • Automatic mode for the fastest fully automatic neuron tracing in 3D
  • Clean Up feature for automatic auditing of tracing; exclusive to Studio package
  • Batch mode for unattended automatic neuron tracing of multiple image files
  • Large volume reconstruction mode for instant navigation and integrated subvolume tracing in very large images
  • Automatic dendritic spine detection, modeling, classification
  • Automatic detection and modeling of putative synapses; exclusive to Studio package
  • Automatic varicosity detection; exclusive to Studio package
  • Image montaging for automated 3D alignment of multiple 3D image stacks
  • Handles big, high-resolution brightfield & fluorescence (wide field, confocal, two-photon & light sheet) images



Vesselucida 360: Quickly and accurately reconstruct microvasculature in 3D and obtain reliable data about the length, connections and complexity of microvessels while generating sophisticated analyses using the built-in analysis software.

Annual subscription includes one license for Vesselucida Explorer and the following features:

  • Full 3D environment for image visualization, rotation and zooming
  • Smart manual mode for targeted manual vessel tracing in 3D
  • User-guided mode for quick and easy semi-automatic vessel tracing in 3D 
  • Automatic mode for the fastest fully automatic vessel tracing in 3D
  • Batch mode for unattended automatic vessel tracing of multiple image files
  • Handles big, high-resolution brightfield & fluorescence (widefield, confocal, two-photon & light sheet) images


Stereo Investigator - Desktop Edition: Provides you with accurate, unbiased estimates of the number, length, area, and volume of cells or biological structures in a tissue specimen. Annual subscription includes the following features:

  • Quantifies number, length, volume, and surface area of cells, structures, and regions
  • Ability to work with 2D and 3D images
  • Provides the ability to perform 2D and 3D analysis of image data acquired with a Stereo Investigator - Microscope Edition system
  • Runs on a separate PC for increased productivity
  • Includes the capability to read in most confocal, brightfield and fluorescent 3D image stacks and provide 3D visualization of your image data


Stereo Investigator—Whole Slide Edition: Unbiased stereology for whole slide images. Specially designed for analyzing large whole slide images. The annual subscription includes the following features:

  • Capable of directly reading most common file formats from slides scanners, including:
▪ Zeiss
▪ Leica\Aperio
▪ Huron
▪ Olympus
▪ Hamamatsu


Stereo Investigator—Cleared Tissue:  Perform unbiased stereology on whole or partial specimens that have been cleared using methods such as CLARITY, 3DISCO, FluoClearBABB, etc. that have been imaged using light sheet, confocal scanning, or two-photon microscopes.

  • Capability to directly read image data from:
▪ light sheet microscopes
▪ confocal microscopes
▪ two-photon microscopes
▪ 3D image stacks 



NeuroInfo: Aligns whole slide images of experiments sections with Allen Mouse Brain Atlas, delineates anatomical regions and automatically detects cells. The software includes the following features:

  • Register serial section images of any orientation to the Allen Mouse Brain Atlas
  • Delineates anatomies in the experimental anatomic space
  • Automatic cell detection and reporting on cell number within selected anatomies
  • Corrects for distortion due to histological processing
  • Combines all image measurements to anatomies in the Allen Mouse Brain Atlas for cross-cohort, or experiment comparisons


TissueMakerAutomatically generate a full resolution 3D reconstruction of any organ or tissue sample from serial sections so that you can easily view cells, structures, and lesions. The software includes the following features:

  • Open and sort multiple virtual slides
  • Specify serial section order across slides
  • Automatic alignment of serial sections with option for manual intervention
  • Automatic correction of upside-down and flipped sections
  • Save registered sections as 3D volumes at selectable output resolutions
  • 3D visualization of aligned volumes
  • read all major whole-slide image file formats



Tissue Mapper: is a comprehensive annotation and delineation tool used for mapping tissue structures. In Tissue Mapper you can:

  • Easily delineate structures at any resolution to create a 3D model from image data
  • Annotate regions of interest from customizable ontology list
  • Map images acquired with brightfield, confocal, two-photon, widefield fluorescence, or light sheet microscopes and with  MRI and microCT
  • Populate custom anatomy lists specific to any organ
  • Visualize completed annotations in Interactive 3D environment 


Microfile+: Uses state-of-the-art compression methods to efficiently and accurately convert 2D and 3D images from almost any source and format into manageable, standardized experimental results. The annual subscription includes the following features:

  • Converts whole slide images, confocal stacks and standard images into the jpeg2000 format.
  • File support for open and zoomable large file, including
▪ MBF JPEG2000
▪ generic TIFF
▪ Vesalius/CaliberID TIFF
▪ Flowview Olympus TIFF
▪ Keyence TIFF
▪ Imaris TIFF
▪ Zeiss LSM
▪ Huron SVS
▪ Leica SVS
▪ CaliberID
▪ HDF5
▪ Imaris IMS
▪ ND2


Professional Technical Support

When you call us you will speak with a person - not an automated system. Talk to us about your hardware, software, or experimental design questions. Our team includes Ph.D. neuroscientists and experts in microscopy, stereology, neuron tracing, and image processing; ready to help you over the phone or online.

We can also custom develop for you

MBF is proud to help bioscience leaders and experts push the next wave of innovation and discovery to benefit humanity. Given this, it’s possible you’re looking for customized technology for your needs. If that is the case, click here to get in touch with us directly. We’d be happy and honored to see if we can create something together that will move all of us forward.

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