Neuroimaging Collaboratory

The Neuroimaging Collaboratory provides resources and support for advanced microscopy and image analysis for BHRI members.


Training and Technical Support:

All users need to complete training on how to use the microscopes or computers prior to scheduling the use of equipment. Training and technical support is provided by the Co-Directors Drs. Aleisha Moore and Lique Coolen.

At present, the Light Sheet microscope is not available for training, but can be used for acquisition of pilot data, with imaging and capture conducted by the collaboratory technician. 

Scheduling and User Fees: 

After completing training, you will receive access to the Elan Infinity scheduling system.

To schedule use of any of the microscopes or computers, use:

How to schedule an instrument on Elan website (after you have been trained).

If you have questions, or for assistance creating an Elan account, please contact Lolita Winning  

The usage will be free for the first six months. We are in the process of proposing fees-for-service to be included in grant proposals. 



Olympus VS200 Research Slide Scanner: 


This Slide Scanner is designed to capture high-resolution images of your microscope slides for quantitative analysis. The slide scanner combines five observation methods (brightfield, darkfield, phase contrast, polarization, fluorescence) to acquire precise fluorescent signals with reduced photo bleaching. The loader holds sample trays for 3" x 1" or 3"x 2" slides and robotic mechanisms quickly and safely load and unload trays while coordinating with the focus and scan unit for fast acquisition. A barcode reader automatically captures and records slide information. 

Fluorescence and bright-field image capturing and analysis: ​ 

stereo-investigatorMBF Bioscience Module Neurolucida is fully integrated with Leica DMR microscope system hardware to control motorized stage, focus, camera, and optical filters, and is used to capture high quality images and z-stacks of brightfield or fluorescent sections. Neurolucida is also specifically designed for accurately tracing neuronal structures directly from histological specimens and generating quantitative morphometric data and is used for over 500 morphological quantitative analyses. Analysis can be completed on a separate computer in the collaboratory (see: Image analysis software). 

Stereo Investigator provides the means to make accurate, unbiased quantification of the number, length, area, and volume of cells, subcellular and macro structures in tissue specimens. It is a key research tool that has helped scientists to make discoveries in numerous areas of neuroscience, as well as other research fields. The Stereo Investigator system makes stereology accessible, with easy-to-follow workflows with the most commonly used probes and clear quantitative results. With Stereo Investigator, stereology can be performed directly on the microscope system, from image stacks, or from whole slide images on a separate computer in the Collaboratory (see: Image analysis software). 

Light-sheet Microscope: Miltenyi Biotec Ultra Microscope II 

lightsheet microscopeThis light-sheet microscope enables rapid 3D visualization of whole biological systems, including embryos, brain and other organs from a variety of animal models or human tissue samples. Homogeneous fluorescent excitation is achieved by six light sheets that illuminate the sample from both sides. Moving the sample through the light sheets allows the generation of sharp and bright 3D images. The light-sheet microscope is compatible with tissue clearing and imaging protocols performed using either aqueous-based solutions (e.g., CLARITY), or organic solvent-based solutions (e.g., 3DISCO, iDISCO). At present, this Light Sheet microscope is not available for training or for individual users, but can be used for acquisition of pilot data, with imaging and capture conducted by the collaboratory technician. 


Image analysis software and computers:

The Collaboratory also includes two stations equipped with Dell computers loaded with image and calcium imaging analysis software. These software packages can be used with images captured on the microscopes in the Collaboratory or other microscopes including any confocal or bright-field/fluorescent microscope:

  • Imaris (Bitplane) Imaris is the market-leading software for visualization and analysis of images collected from wide-field, confocal (including spinning disk), light sheet, two-photon, electron microscopy, CLEM, OPT, and other microscopes, with over 4,000 publications in 2020 alone.
  • Deconvolution software (Olympus)
  • Stereo Investigator (MBF Bioscience)
  • Neurolucida (MBF Bioscience)
  • Calcium Imaging Analysis software (Inscopix)

Contact Us:

To schedule training or technical support, please email Lique Coolen:

To schedule a consultation on study design, use of instrumentation or image analysis, please email:

Lique Coolen:

Aleisha Moore: