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Imaging Software

MBF Bioscience

MBF Bioscience Microbright field Spot

MBF Bioscience design quantitative imaging software for stereology, neuron reconstruction and image analysis, integrated with the world’s leading microscope systems to empower your research. Their development team and staff scientists are actively engaged with leading bioscience researchers, constantly working to refine their products.

Website: https://www.mbfbioscience.com

MBF Bioscience Microbright field NeuroInfo

NeuroInfo®

Intelligent Brain-Wide Cellular Screening with Anatomic Specificity

NeuroInfo performs brain-wide analyses of cells and biochemical markers, and automatically categorizes them in neuroanatomical regions. Uses advanced deep learning methods – no more manually clicking cells or hand drawing anatomic boundaries.It works with specimens imaged with Brightfield, Widefield fluorescence and Confocal.


Automatically Register Histological Sections and Associated Data to the Allen Mouse Brain Atlas

With NeuroInfo, researchers can automatically identify and delineate brain regions within experimental mouse brain sections. NeuroInfo replaces the tedious manual process of neuroanatomical identification; no more paging through a reference atlas to match experimental images, and manually delineating anatomies in images.



NeuroInfo, Align Data to the Allen Mouse Brain Atlas, Whole Brain Reconstruction, Cell Detection
NeuroInfo
  • Aligns whole slide images of experimental tissue sections to the Allen Brain Atlas
  • Delineates anatomical regions in experimental sections
  • Detects cells within the anatomical regions
  • Aggregates measurments from within anatomical regions
  • Maps all image measurements to anatomies in a standardized atlas space so that results can be compared across animals, experiments, and laboratories
Automatic Cell Detection and Mapping
Automatic Cell Detection and Mapping

Identify labelled neurons in whole slide images using an intuitive cell detection workflow. The sophisticated detection algorithm is robust against histologic and imaging artefacts such as edge effects, uneven illumination, and variable staining across specimens. Detected cells can be mapped to the Allen Mouse Brain Atlas and tallied in each of its 2500 brain structures, making comparative quantitative analysis between mice from different experiments and laboratories easy and standardized.

 
 

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MBF Bioscience Microbright field Stereo Investigator

Stereo Investigator


Count Cells and Quantify Lengths, Areas, and Volumes with the World’s Best and Most-Cited Stereology System

A Stereo Investigator system provides you with accurate, unbiased estimates of the number, length, area, and volume of cells or biological structures in a tissue specimen. It is a key research tool that has led to advances in numerous areas of neuroscience including neurodegenerative diseases, neuropathy, memory, and behaviour, as well as other research fields including pulmonary research, spinal cord research, and toxicology.

With Stereo Investigator, stereology can be done on a microscope system from image stacks, or from whole slide images. It is compatible with Brightfield, Multi-Channel Fluorescence, Confocal, and Structured Illumination Microscopes.

Stereo Investigator has been cited in over 7,000 published research papers

Stereo Investigator Works with Brightfield, Multi-Channel Fluorescence, Confocal, and Structured Illumination Microscopes

Stereo Investigator fully integrates with your microscope and associated hardware to reduce manual work and to speed up data collection. It can:

  • direct motorized microscope stages to automatically move in order to perform systematically random sampling of tissue specimens
  • control cameras so you can view live images or collect and save images and image stacks, even change or save camera settings for future use
  • control the focus position, change objective lenses or adjust the condenser
  • automatically change filter wheels and mirror cubes when acquiring fluorescent images or image stacks

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Slide Scanning Workflow

A completely new slide scanning workflow is easier to use, will save time training new users and give you great slide scanning results. Use this workflow to scan at any magnification and create high resolution 2D images or 3D stacks. This workflow brings all the controls and features necessary to complete slide scanning into one location. Feature includes:

  • An easy-to-follow guide that makes it simple for new users to scan great quality images
  • Background correction to insure clean, even, image quality
  • Heat map allows you to spot folds and other areas that need additional focus sites
  • Validate your settings before you start a long acquire by taking a test image
Stereology from Image Stacks
Stereo Investigator Image Stacks

Performing stereology at the microscope from fluorescent tissue specimens can be problematic since exposure to light degrades fluorescent tissue. With Stereo Investigator you can acquire image stacks using systematic random sampling (SRS) – a method that produces image stacks suitable for stereology- and then perform stereology on the image stacks. A great benefit of stereology on image stacks is that you can run many probes for different types of analyses and never have to worry that your tissue will fade. Plus, it’s easier to double check the analysis.

During SRS image stack acquisition, Stereo Investigator directs the motorized stage, camera, and, for fluorescent images, the filter wheels and mirror cubes. This means you can automatically capture image stacks at each sample site, and then take the image stacks to a computer with Stereo Investigator Desktop and perform stereological analysis.

Stereology on Whole Slide Images
Stereo Investigator Whole Slide Images

Whole slide images give you the freedom to perform stereology on a computer away from the microscope. Stereology on 2D whole slide images can be employed for counting cells with the Physical Fractionator, quantifying area and volumes with the Cavalieri probe, and for calculating the area of a small objects, such as lesions or plaques, within a larger region using the Area Fraction Fractionator.

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Stereology on Cleared Tissue Specimens
Stereo Investigator Cleared Tissue Specimens

Stereo Investigator – Cleared Tissue Edition is the gold standard in unbiased stereology for use on cleared tissue. It allows researchers to use the world’s most cited stereology software to analyze intact, cleared tissue specimens imaged with light sheet or confocal microscopes.

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Stereo Investigator Add-On Modules
  • Image Montaging – Digitally re-create a complete region of interest or an entire specimen in 3D or 2D for analysis, archiving or sharing
  • Image Stacks – Capture and analyze 3D image stacks
  • Structured Illumination – An Affordable, Fully Integrated Quantitative Confocal System
  • 2D Slide Scanning – Create, view, and analyze an entire specimen in a single high-resolution image
  • 3D Slide Scanning – 3D Whole Slide Imaging for image analysis, sharing or archiving
  • MRI – Analyze MRI image sets and apply stereological techniques
  • 3D Serial Construction – Perform 3D reconstructions from serial sections.
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Neurolucida®360


Automatic 3D Neuron Reconstruction and Quantitative Analysis

Neurolucida 360 is a 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.

With the sophistication to analyze specific neuronal structures such as axons, basal dendrites, apical dendrites, and axon-carrying dendrites, you can completely reconstruct and analyze any neuron in any species.

The most advanced image detection algorithms allow you to confidently reconstruct cells using a variety of labelling and microscopy techniques.

 

Quantify Neuronal Morphology

Automatic neuron reconstruction for creating and analyzing realistic, meaningful, and quantifiable neuron reconstructions from microscope images. Perform detailed morphometric analyses of neurons, such as quantifying:

  • the number of dendrites, axons, nodes, synapses, and spines
  • the length, width, and volume of dendrites and axons
  • the area and volume of the soma
  • the complexity and extension of neurons
Automatic Detection and Modeling

Neurolucida 360 is uniquely designed to automatically model, classify and quantify dendritic spines in 3D. Spines are automatically classified by type (i.e., mushroom, filipodia, stubby, thin as described in the scientific literature). It is also designed to model and quantify somas, varicosities, and synapses.

  • Detect and Classify Spines
  • Trace Branches and Detect Varicosities
  • Trace Golgi Stained Neurons
  • Reconstruct Neurons from Cleared Tissue
 

Real-time Interactive 3D Visualization

As you work with increasingly bigger and more complex image data, high performance 3D visualization has become indispensable to effective data interpretation.

MBF’s software includes a highly versatile 3D visualization environment suitable to most microscopy images with state-of-the-art functionalities to support your analysis and publication needs.

  • Visualize large, complex 3D images (including multichannel images) and reconstructions
  • 2D and 3D image data from two-photon, confocal, brightfield or light sheet microscopy
  • 3D volume, image slicing, and simultaneous views
  • Multiple projections: XY, YZ, XZ, alpha, minimum, and maximum
  • Transparency, rendering (wireframe, centerline, surface, texture) and other display options for image and traces than can be adjusted on the fly
  • Create dynamic movies
  • Export options including exporting 3D graphics to third-party applications
  • Loads complex surfaces in seconds
  • Works with the most advanced “gaming class” graphics cards to deliver high performance at an affordable price
 

How can Neurolucida 360 help you?

Image courtesy: Confocal microscopy image of a human neocortical neuron injected with Lucifer Yellow, showing 3D-reconstructed dendrites and spines superimposed on the confocal image. Authors: Ruth Benavides-Piccione, Isabel Fernaud, Asta Kastenauskaite and Javier DeFelipe.

  • Run analyses that exactly match your research questions
  • A ready to use solution with no need for programming skills or the creation of supplementary scripts (e.g., MatLab)
  • Use it on a wide range of research specimens, from the sub-micrometer level (synapses) to the macrolevel (mapping projection neurons)
  • Use the stains and visualization techniques that fit your research paradigm including Golgi, 2D, expansion microscopy, clarity, iDISCO, uDISCO, confocal, two-photon
  • Work with equipment in your facility, virtually all microscope image formats are supported
  • Consult with our expert neuroscientists to get recommendations on the best means to analyze your experimental data

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Biolucida®

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.

MBF Bioscience and their Biolucida systems can help you with:

  • Data from 2D/3D slide scanners, confocal Z-stacks, lightsheet whole brain images
  • Data Storage and Management
  • Data Access and Security
  • Data Analysis and Visualization
Biolucida Medical Education Edition
Medical Education Edition

Enrich your medical education course with Biolucida — interactive learning management software developed in collaboration with leading medical educators. Biolucida takes the concept of virtual microscopy to the next level by providing educators a collaborative platform to manage, display, annotate, and navigate whole slide images. Reach more students efficiently by delivering dynamic and rich content accessible by hundreds of users simultaneously.

Biolucida Research Edition
Research Edition

Whole-slide scanners, confocal and light sheet microscopes have the ability to create vast image sets that can be challenging to view and manage. They are often comprised of very large files, potentially reaching hundreds of gigabytes in size. These images, generated from a variety of microscopes and slide scanners that produce different file formats, cause compatibility issues in viewing, collaboration, and analysis. Biolucida solves these challenges.

Biolucida Publisher Edition
Publisher Edition

With Biolucida, scientific journals can publish entire high-resolution 2D and 3D image data sets in research papers. A wide variety of image data can be presented, including whole slide image series (virtual slides) from entire organs, 3D images of tissue cleared with CLARITY, iDISCO, and other clearing methods, 3D reconstructions of whole slide images, high-resolution image montages, and much more.

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TissueScope


Fast and Versatile Slide Scanner Designed for Neuroscience Research

The TissueScope, engineered in collaboration with Huron Digital Pathology, is a fast and versatile whole slide scanner that is super-charged with MBF Bioscience big data handling technology to easily stream high quality image data to quantitative analysis with all of MBF Bioscience software.

TissueScope
Key features:
  • Brightfield slide scanner that handles up to twelve, 1”x 3” (25mm x 75mm) slides, six, 2” x 3” (50mm x 75mm) slides or any single slide up to 6” x 8” (150mm x 200mm)
  • Handles large specimens, such as human brain sections, that most other scanners can’t handle
  • For 60 micron section, slides containing an entire mouse brain can be mounted in a single tray
  • Fast: <1 minute per slide (15mm x 15mm section at 20x)
  • High Resolution: 0.2 at 40x, 0.4 at 20x with optical resolution of 0.75na
  • Versatile: 2D and 3D slide scanning
  • Easy to Use: Automatic tissue detection and automatic focus
  • Easy to Manage: Image-based barcode reading
  • Big Data Handling: File format optimized for streaming with Biolucida image server and for analysis
  • Optional slide loader capabilities to easily scan up to 120 standard or 60 double-wide slides, or even larger slides up to 6″ x 8″

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MBF Bioscience Microbright field Neurolucida

Neurolucida


The Most Advanced System for Neuron Tracing and Reconstruction, Quantitative Neuron Analysis, and 3D Brain Mapping

Neurolucida is a microscopy system specifically designed for performing accurate neuron reconstructions directly from histological specimens. It is capable of over 500 quantitative morphometric analyses, including:

  • the number of dendrites, axons, nodes, synapses, and spines
  • the length, width, and volume of dendrites and axons
  • the area and volume of somas
  • the complexity and extension of neurons
Neurolucida Works with Brightfield, Multi-Channel Fluorescence, Confocal, and Structured Illumination Microscopes

Microscopy hardware and Neurolucida software work in harmony to deliver a powerful, seamless neuron reconstruction system. A typical system includes a microscope, computer, and Neurolucida software. Most of what is visible through the oculars is displayed on the computer monitor with Neurolucida.

Neurolucida fully integrates with your microscope and associated hardware to reduce manual work and to speed up data collection. It can:

  • control motorized stages
  • control cameras to change or save settings for future use
  • operate the focus knob or change objectives
  • change filter turrets, filter wheels, and mirror cubes when acquiring fluorescent images or image stacks

Neurolucida has been cited in over 6,000 published research papers.


3D Brain Mapping
3D Brain Mapping

Neurolucida has advanced tools for creating and analyzing 3D reconstructions of brain and spinal cord specimens.

  • Map and analyze a long neuronal pathway
  • Map the distribution of cells in a region of interest
  • Quantify volume for studies looking at volume change, such as the atrophy of the striatum in a specimen that has the Huntington’s gene expressed, or the volume of lesions that appear in a region of interest.
  • Analyze the distribution of objects in a region of interest and find the proximity of one object to another or find the distance between the object and an anatomical boundary.
  • Read about how scientists used Neurolucida to map memories
Serial Section Reconstruction
Serial Section Reconstruction

Serial sections are tissue sections that have been cut sequentially with a microtome. To obtain morphometric data about neurons or structures that extend beyond a single tissue section, researchers often create a serial section reconstruction – a digital representation of the serial tissue sections. This method includes tracing the outline of each tissue section at low magnification and tracing the neuron or structure of interest in each tissue section at a higher magnification. This can be done at the microscope or from images with Neurolucida, which has tools to help make this process easier. For example, Neurolucida has an automatic contouring tool to help you trace the outline of the tissue specimen or trace an anatomical boundary within the specimen.

Capture Image Stacks and Whole Slide Images with Neurolucida
Capture Image Stacks and Whole Slide Images with Neurolucida

Neurolucida can capture 2D (x,y) and 3D (x,y,z) whole slide images (high resolution digital images of your specimen) with the addition of the 2D or 3D Slide Scanning Module, but Neurolucida also supports whole slide images from providers such as Aperio and Hamamatsu. Working with whole slide images gives you the freedom to create neuron reconstructions and analyze them on any computer (even those not connected to a microscope), and also gives you a permanent digital file of your specimen that can be easily stored on Biolucida, MBF’s image viewing, sharing, and storing application.

Automatic Cell Detection and Mapping
Automatic Cell Detection and Mapping

Identify labeled neurons in whole slide images using an intuitive cell detection workflow. Our sophisticated detection algorithm is robust against histologic and imaging artifacts such as edge effects, uneven illumination, and variable staining across specimens.

Neurolucida Add-On Modules
  • Image Montaging – Digitally re-create a complete region of interest or an entire specimen in 3D or 2D for analysis, archiving or sharing
  • Image Stacks – Capture and analyze 3D image stacks
  • Structured Illumination – An Affordable, Fully Integrated Quantitative Confocal System
  • 2D Slide Scanning – Create, view, and analyze an entire specimen in a single high-resolution image
  • 3D Slide Scanning – 3D Whole Slide Imaging for image analysis, sharing or archiving

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WormLab


WormLab is a system for imaging, tracking, and analyzing C. elegans and other worms. It has a user-friendly software interface with a powerful model-specific tracking algorithm that collects data about a single worm or multiple worms, even through omega bends, reversals, and entanglements. The algorithm analyzes virtually any video file type, including .avi, .wmv, and .mp4.

Key features:
  • Multiple Worm Tracking from video files
  • Track selected worms, or all worms in the frame
  • Differentiate the behavior of single or multiple worms via robust, patented algorithms identifying:
    • Entanglements & Omega bends
    • Reversals & Pirouettes
    • Coiling & Self-overlap
    • Swimming & Thrashing
  • Track at high, medium, or low magnification
  • Advanced worm model with peristaltic progression movement including elongation
  • Multiple-hypothesis tracking results in improved worm tracking
  • Discriminates between head and tail using both curvature and motion direction
  • Selective viewing of worm outlines, midpoints, tracks, and head/tail markers
  • Export locomotion data to Microsoft Excel
  • Built-in workflow guides you through each step to acquire, track & analyze image data from the WormLab System or your own acquisition system
  • Load video files from disk or directly from a connected camera with optional camera control
  • Support for hundreds of different video codecs included

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BrainMaker®


Automatically Align Sections to Visualize Brains in 3D

Use BrainMaker to assist you with cell mapping, cytoarchitectonics and other areas requiring the characterization of neuronal circuitry to create a comprehensive anatomical reference. BrainMaker automatically creates full-resolution, 3D reconstructions of the entire brain (or any organ) from serial sections of whole slide images. It allows you to easily view cells, structures, and lesions. With just a glance, you can locate neurons expressing a particular gene or visualize axonal projections of specific neurons with full anatomical context.

Go From This
BrainMaker
 
To This
BrainMaker


Quantify Your Data

Use the 3D anatomical reference created with BrainMaker to make measurements within the entire organ, something that was not possible using the serial sections directly. Analyze the size and shape of neuronal structures within the 3D reconstruction using Neurolucida 360. Or assess cell distribution within a lesion using stereology with Stereo Investigator.


View, Store and Share Your Whole-Slide Images and 3D Reconstructions

Reconstructions created with BrainMaker can be stored, viewed, and shared with Biolucida – our platform for organizing and sharing big image data. Never run out of storage space, or spend hours searching for an image again. And instead of publishing a 2D image of your 3D reconstruction, you can share the actual 3D reconstruction and allow others to dynamically visualize it using our free Biolucida 3D image viewer.

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Vesselucida®360


Quantify Microvasculature Accurately and Efficiently

Vesselucida 360 quickly reconstructs microvasculature in 3D to obtain reliable data about the length, connections, and complexity of micro vessels. The breakthrough software’s quantitative analysis tools are designed to empower researchers studying cancer, diabetes, strokes, and other conditions that affect microvasculature.

Quantify:

  • Changes in vasculature due to traumatic brain injury or stroke
  • Changes in blood vessels of the retina due to diabetes (diabetic retinopathy)
  • New blood vessels due to a cancerous tumour (angiogenesis)
A Comprehensive Solution to Analyze Microvasculature

Vesselucida works with a wide array of 3D images, even large 3D images of intact tissue specimens. Once your reconstruction is complete, you can obtain a comprehensive morphological profile.

  • Reconstruct microvascular structures in 3D accurately and fast
  • Built-in analyses means no need for programming skills or the creation of supplementary scripts (e.g., MatLab)
  • Metrics for comprehensive morphological analyses: Segments and nodes counts, frequency of anastomoses, vessel surface and volume, and more
  • Consult with our staff scientists to determine the best course of action to make sense of your data
Automatically Reconstruct Vasculature

The sophisticated software algorithms in Vesselucida 360 were developed specifically to take into account vascular loops.

Compare with Ground-Truth Data

Vesselucida 360 also includes a full suite of tools to manually trace and edit your reconstruction to create a ground-truth representation of your vascular data. You can also fine-tune and correct the automatic reconstructions in cases of particularly challenging image data.

Metrics to Answer Your Research Questions

Our rigorously tested analyses provide accurate and relevant results that you and others can trust for publications. Use Vesselucida Explorer, our Vesselucida 360 companion analysis software, to perform sophisticated analyses that help answer your research questions.

Vesselucida Explorer provide vasculature-specific metrics such as segments and nodes counts, frequency of anastomoses, vessel surface and volume, and more.

Real-Time Interactive 3D Visualization

As you work with increasingly bigger and more complex image data, high performance 3D visualization has become indispensable for effective data interpretation.

MBF’s software includes a highly versatile 3D visualization environment suitable to most microscopy images with state-of-the-art functionalities to support your analysis and publication needs.

  • Visualize large, complex 3D images (including multichannel images) and reconstructions
  • 2D and 3D image data from two-photon, confocal, brightfield or light sheet microscopy
  • 3D volume, image slicing, and simultaneous views
  • Multiple projections: XY, YZ, XZ, alpha, minimum, and maximum
  • Transparency, rendering (wireframe, centerline, surface, texture) and other display options for image and traces than can be adjusted on the fly
  • Create dynamic movies
  • Export options including exporting 3D graphics to third-party applications
  • Loads complex surfaces in seconds
  • Works with the most advanced “gaming class” graphics cards to deliver high performance visualization at an affordable price
 

Learn More »

 
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Vesselucida® Microscope Edition


Model and Quantify Microvasculature Accurately

Vesselucida Microscope Edition is a unique product specifically designed to reconstruct and analyze microvascular networks by controlling microscope hardware so you can trace directly from slides. Built-in analysis tools will provide you with the information you need for your studies on cancer, diabetes, strokes and other conditions that affect microvasculature.

  • Changes in vasculature due to traumatic brain injury or stroke
  • Changes in blood vessels of the retina due to diabetes (diabetic retinopathy)
  • New blood vessels due to a cancerous tumor (angiogenesis)
Vesselucida on a Microscope

Microscopy hardware and Vesselucida software work in harmony to deliver a powerful, seamless vessel reconstruction system. A typical system includes a microscope, computer, and Vesselucida software. Most of what is visible through the oculars is displayed on the computer monitor with Vesselucida.

Vesselucida fully integrates with your microscope and associated hardware to reduce manual work and to speed up data collection. It can:

  • control motorized stages
  • control cameras to change or save settings for future use
  • operate the focus knob or change objectives
  • change filter turrets, filter wheels, and mirror cubes when acquiring fluorescent images or image stacks

Learn More »