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Imaging Software

MBF Bioscience

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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

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Stereo Investigator

Stereo Investigator

Count cells and quantify lengths, areas, and volumes with the world’s best and most-cited stereology system.

Stereology is considered in most biological sciences to be the most accurate and efficient way to estimate the number, length, and volume of cells.

A Stereo Investigator system for stereology gives you 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 helped lead advances in numerous areas of neuroscience including neurodegenerative diseases, neuropathy, memory, and behavior, as well as other research fields including pulmonary research, spinal cord research, and toxicology.

Stereo Investigator has been cited in over 4,000 published research papers.

Unbiased stereology with Stereo Investigator – Overview

Extension Modules
  • Virtual Tissue 2D – Create 2D whole slide images
  • Virtual Tissue 3D – Create 3D whole slide images
  • Image Stack and 3D Visualization – Acquire and view 3D image stacks suitable for stereology
  • Image Montaging – Automated 3D montaging/stitching of image stacks
  • MRI Support – Analyze MRI image sets
  • Serial Section Reconstruction – 3D anatomical reconstructions from serial sections
  • Deconvolution – Deconvolution of brightfield, widefield fluorescence, and confocal images
  • Structured Illumination – Control of structured illumination hardware such as the Zeiss Apotome
  • Zen Control – Unbiased cell counting/stereology on a Zeiss LSM confocal microscope
  • Open Confocal – Unbiased cell counting/stereology on a confocal microscope
  • Fluoview – Unbiased cell counting/stereology on Olympus Fluoview 300 & 500

More information at MBF Bioscience’s website: click here

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An advanced system for neuron tracing and reconstruction, neuron analysis, and 3D brain mapping

Analyze the structure of neurons by tracing them in 3D with Neurolucida. Trace neurons at a microscope from a physical slide, or at a computer with image stacks. Obtain a wide variety of quantitative data about dendrites, axons, nodes, synapses, and spines.

Neurolucida is advanced scientific software for brain mapping, neuron reconstruction, anatomical mapping, and morphometry. Since its debut more than 20 years ago, Neurolucida has continued to evolve and has become the worldwide gold-standard for neuron reconstruction and 3D mapping. Researchers have reconstructed tens of thousands of neurons using our technology.

The user-friendly interface gives you rapid results, allowing you to acquire data and capture the full 3D extent of neurons and brain regions. You can reconstruct neurons or create 3D serial reconstructions directly from slides or acquired images, and Neurolucida offers full microscope control for brightfield, fluorescent, and confocal microscopes.

Neurolucida is available in two separate versions: Standard, which controls research microscope hardware and Workstation, for offline analysis away from the microscope. The software provides automatic analysis of hundreds of quantitative parameters, with results presented in graphical and spreadsheet format, all exportable to Microsoft Excel ®.

More information at MBF Bioscience’s website: click here

Extension Modules


AutoNeuronAutoNeuron traces neurons from image stacks or whole slides in minutes, significantly reducing time and effort. AutoNeuron works with brightfield, widefield fluorescence, and confocal images.


AutoSpineAutoSpine is a ground-breaking tool for automatic detection and quantification of dendritic spines. Using high-quality dendritic tracings from AutoNeuron or Neurolucida, AutoSpine identifies and counts the spines along the traced dendrites.


AutoSynapseAutoSynapse, an extension module for Neurolucida, automatically detects and analyzes pre-synaptic markers such as synaptophysin and post-synaptic markers such as PSD95, then uses nearby dendrites traced with AutoNeuron or Neurolucida to analyze which of those synaptic markers are associated with particular dendrites.

Other Modules

AutoSynapse, an extension module for Neurolucida, automatically detects and analyzes pre-synaptic markers such as synaptophysin and post-synaptic markers such as PSD95, then uses nearby dendrites traced with AutoNeuron or Neurolucida to analyze which of those synaptic markers are associated with particular dendrites.

  • Virtual Tissue 3D for creating 3D whole slide images
  • Virtual Tissue 2D for creating 2D whole slide images
  • Image Montaging for automated 3D montaging/stitching of image stacks
  • Image Stack and 3D Visualization for acquiring and viewing 3D image stacks
  • Deconvolution for the deconvolution of brightfield, widefield fluorescence, and confocal images
  • Structured Illumination for integration with structured illumination microscopy hardware
  • Zen control for integration with Zeiss LSM confocal microscopes
  • Open confocal control for integration with confocal microscopes
  • Fluoview control for integration with Olympus Fluoview 300 & 500.

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Neurolucida 360

A new paradigm for automatic neuron reconstruction

With Neurolucida 360, you can automatically reconstruct neurons and detect spines and synapses in a 3-dimensional environment to obtain reliable data about the size, shape, and complexity of neurons. Neurolucida 360 works with 3D and 2D images acquired with confocal, two-photon, and fluorescence microscopes or slide scanners. And it excels at handling very large images such as whole slide images or images of tissue cleared with CLARITY, Scale, iDISCO, and more.

Quickly reconstruct somas, dendrites, and axons

Neurolucida 360 allows you to collect more data in less time. The user-guided tracing method in Neurolucida 360 helps you trace neurons quickly and uniformly. Find the soma and click it to reconstruct the soma volume. Locate a dendrite or axon and move your cursor along it – the algorithm will find the thickness of the process. Edits can easily be made in the 3D environment.

Incredibly fast 3D spine detection and classification

Dendritic spine detection and classification are fully automatic in Neurolucida 360. Simply click ‘detect all’ to reconstruct all spines in the image, and then click ‘classify all’ to classify spines into one of four spine types. Edits can easily be made in the 3D environment.

Reconstruct neurons 15 times faster with Neurolucida 360

Would you rather spend 1 hour and 3 minutes reconstructing a neuron, or just 4 minutes? To see how fast Neurolucida 360 really is, we had an experienced Neurolucida user trace a neuron manually with Neurolucida and then with Neurolucida 360. The manual reconstruction took 1 hour and 3 minutes. The reconstruction with Neurolucida 360 took just 4 minutes. If you have to reconstruct 10 of these neurons it would take you 10 hours and 30 minutes, or just 40 minutes with Neurolucida 360. Use the extra 9 hours and 50 minutes to mine the wealth of morphometric data.

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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.

Capturing videos with a WormLab system

Capturing high-quality videos is essential for obtaining accurate analyses as quickly as possible. To do this, a complete WormLab system includes the following hardware:

1) Video cameras to acquire videos directly with WormLab

2) An illuminator to project smooth, even light onto your plates

3) A specially designed camera stand to securely hold the camera in the exact location you want.

WormLab Features
  • Multiple Worm Tracking from video files
  • Track selected worms, or all worms in the frame
  • Track worms through entanglements and overlap
  • 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 makes it easy to run WormLab and gather data efficiently
  • Load video files from disk or directly from a connected camera with optional camera control
  • Support for hundreds of different video codecs included
Analyses – More than 10,000 measures to analyze your specimens

WormLab presents the tracking data in a multi-tabbed table format. Export all data to Microsoft Excel or cut-and-paste portions to any other application. Frame-by-frame detail data is provided for each worm track as well as track summary data. Analysis output includes:

  • Worm Position (Head, midpoint and tail) frame-by-frame
  • CenterLine Points (variable resolution, selected by user)
  • Speed (instantaneous and moving average)
  • Body Area
  • Body Wavelength
  • Track Length
  • Direction
  • Body Bending Angles
  • Head Bending Angle
  • Omega Bend Detection
  • Reversal Detection

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With BrainMaker you can now see labeled cells and structures or view lesions throughout a true 3-dimensional reconstruction of the entire brain (or any organ). At a single glance you can see the location of all neurons expressing a particular gene, visualize axonal projections of specific neurons within the full anatomical context.

How BrainMaker works

BrainMaker generates high-resolution 3D reconstructions from serial sections imaged with whole slide scanners and research microscopes. Load the images into BrainMaker and then direct your attention to other projects while BrainMaker automatically detects the individual sections on each slide, and then aligns the sections to create the full 3D image reconstruction.

It’s fast. And it’s smart. If you mount a section upside down, BrainMaker will automatically correct it during the alignment process. BrainMaker uses innovative computational algorithms to align image features found in multiple serial sections. If additional adjustments need to be made to the automatic alignment, researchers can easily edit the 3D reconstruction.

Watch an overview of how BrainMaker works

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Live Cell Imaging, Low Light Imaging


Analyze autoradiography and optical density

Densita manages your autoradiography study with the most efficient workflow available.

First-time users can be productive with our intuitive technology, which includes specific steps for acquiring images, calibrating, linking total- and non-specific binding images, outlining regions, and exporting results to Microsoft Excel ®.

Using an optical step wedge or radioactivity standards, Densita quickly and efficiently calculates ROD (relative optical density), luminance, concentration, the area of your region of interest, ligand concentration, and the amount of radioactivity.

Densita can acquire new images, load previously-saved images, or read your existing MCID files. It also includes the ability to montage, and it supports multi-channel fluorescence images.

Another feature that sets Densita apart is its ability to automatically recalculate your results any time you adjust the data, at any point in the workflow. There is no need to recapture the image or start over from the beginning. Simply make the change, and Densita will re-do the work for you.

See what our complete autoradiography system can do for your lab.

Download brochure

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Live Cell Imaging, Low Light Imaging


For microscope control and image acquisition

Our newest product, Microlucida, builds on our core software framework of Neurolucida and Stereo Investigator, and provides all the tools necessary for advanced microscope control and image acquisition for brightfield, fluorescence, and confocal systems. It is the ideal application for research scientists who need to capture images in 2D, 3D, and 4D.

Microlucida gives you the power to acquire images from multiple fields of view and create seamless image montages, known as virtual slides. It also enables you to use a single high-quality image acquisition application across all of your microscopes, a feature particularly beneficial for core facilities.

Microlucida can save large amounts of disk space with its high-quality JPEG 2000 compression of images and stacks. Microlucida also enables time-lapse image acquisition over multiple channels.

With support for research microscopes from Zeiss, Olympus, Nikon, and Leica, Microlucida is also custom-designed for seamless integration with the world’s leading motorized stages and cameras.

Capture images easily with Microlucida.