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Additional resources at the facility include multiple computer workstations with installed software for image visualization and analysis (also available for download), a sample preparation laboratory, and supplementary microscope objectives.


We have four computer workstations dedicated to viewing and processing of large, image datasets acquired with the facility's instruments, particularly the light sheet microscopes. A suite of imaging software (below), including a full version of Imaris, is installed and also available for download. Please contact us for assistance or to install additional software.


Image Acquisition and Visualization Software

  • Zen Blue and Zen Black: Software for controlling Zeiss widefield and laser scanning microscopes, respectively; they also serve as user-friendly image processing programs with methods for airyscan processing, spectral unmixing, batch processing, orthogonal projection, and stitching.
    • Zen Lite: A free, stand-alone version for viewing .czi files with limited processing features.
  • NIS-Elements AR: Software for controlling Nikon microscopes; it also serves as a user-friendly image processing program with tools for good 3D/4D visualization and High Content Analysis (HCA).
    • NIS-Elements Viewer: A free, stand-alone version to view .nd2 files with limited processing features.
  • Solis (available upon request): Software platform designed for image capture and analysis with Andor cameras.
  • Micro-manager: An open-source software package for control of most automated microscopes, cameras, and peripherals. It offers an intuitive interface as a plugin to ImageJ.
  • CaseViewer: Digital microscope viewer for use with 3DHISTECH slide scanners with slide stack visualization and MultiView features.
  • Pannoramic Viewer: Digital microscope viewer for use with 3DHISTECH slide scanners.
  • Nanozoomer Digital Pathology (NDP.view2): Digital microscope viewer for use with Hamamatsu format slides.
  • IrfanView: A popular, free graphic viewer commonly used for digital microscopy slides.
  • Biolucida Viewer: A free viewer commonly used for large multi-dimensional datasets such as virtual slides.
  • TissueFAXS Viewer (available upon request): A stand-alone program for visualization of IHC/IF staining of digital slide images obtained with the TissueGnostics TissueFAXS 200 slide scanner.
  • VLC: A free, cross-platform multimedia player that plays most multimedia files as well as DVDs, Audio CDs, and various streaming protocols.  

Image and Photo Manipulation Software

  • Adobe Photoshop and Adobe Illustrator (available on Workstation #2): Raster- and vector-based graphics editors, respectively, offering a variety of powerful tools with multiple image-editing functions. They are the de facto industry standard in photo manipulation and often used for publishing.
  • GNU Image Manipulation Program (GIMP): A free, open-source, cross-platform image editor providing sophisticated tools along with 3rd party plugins for graphics design.
  • paint.NET: A free, open-source image and photo editing application with an intuitive user interface supported by 3rd party plugins.
  • yEd: A free, open-source, cross-platform graph editor used to quickly and effectively generate high-quality diagrams.

Image Analysis Software and Programming Tools

  • Imaris (available on Workstation #1): The leading image visualization and analysis software capable of interactive 3D/4D rendering for large, multi-channel, microscopy datasets. Analysis includes cell counting, cell tracking, neuron tracing image segmentation, co-localization, and 4D movie generation. It has plugin capabilities for integrating custom-written macros from MATLAB, ImageJ, Python, etc. 
    • Imaris Stitcher: A stand-alone application made for precise alignment and three-dimensional fusing of multiple microscopy image tiles into one 2D, 3D, or 4D volume.
  • Vision4D (available on all Workstations): Image visualization and analysis software capable of interactive 3D/4D rendering for large, microscopy datasets.
  • Strataquest (available on Workstation #3): Image analysis and visualization software for automated detection/cytometry and context-based quantification tasks across entire slides.
  • ImageJ: A popular free, open-source Java application that offers versatility for image processing via custom acquisition, analysis, and processing plugins.
    • Janelia custom-written macros are available: Intensity Modulated Display (IMD)
    • FIJI: An extended distribution of ImageJ with many bundled 3rd party plugins featuring an integrated updating system.
  • Icy: An open-community platform for bioimage informatics, providing software resources to visualize, annotate, and quantify bioimaging data with native ImageJ integration.
  • Cell Profiler: An open-source Python application developed to facilitate high content image analysis; no programming knowledge required.
  • ilastik: An open-source Python application for image classification, segmentation, and analysis; no previous experience in image processing required.
  • BioImageXD: An open-source C++ application for attractive visual display of 3D/4D image datasets.
  • FluoRender: An open-source interactive rendering tool for attractive visual display of 3D/4D image datasets that also supports advanced segmentation.
  • Vaa3D: An open-source application for real-time 3D visualization and quantitative analysis of large-scale image datasets.
  • NeuronStudio: A free platform that provides tools for 2D/3D visualization as well as manual and automatic detection/tracing of dendritic structures.
  • MATLAB (available on all Workstations): A multi-paradigm, numerical computing environment and proprietary programming language that allows matrix manipulation, advanced plotting, implementation of algorithms, creation of user interfaces, etc. Multiple, specialized toolboxes are available.
  • Python: An interpreted, object-oriented, high-level programming language with dynamic semantics. It has an extensive, freely-distributed, standard library that supports modules and packages which encourages program modularity and code reuse.

Additional software titles are available from the Janelia Software Catalog.

Sample Preparation Lab

We have multiple lab benches for simple sample preparation work including a supply of various materials and disposables. Outside chemicals can be stored in the designated cabinets. Please exercise appropriate lab safety, i.e., disposal of used chemicals and waste container replacement. A fume hood, Milli-Q water purification system, refrigerators (20°C), centrifuge, and hybridization oven are also available on site.





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