(SW5) Image Processing and Analysis for Core Facilities

Location: Room 216

Please join us for a full day hands-on workshop on image processing for microscopy. The morning will cover general image processing fundamentals focusing on open-source and commercial software solutions to better understand their cabibilites and how they may fit into your portfolio.  CellProfiler, arivis, Amira, Nikon Elements and Ionpath (multi-spectral) will all be there for participants to experience. After an introduction to the key concepts and requirements to host image analysis tools there will be rotating sessions will allow people to join topical groups covering a range of different image processing (including automation, multi-dimensional visualization, colocalization, decovolution, big-data visualization and more!).

  • The workshop will be combination of morning lectures and hands-on training – please bring your laptops for the hands-on portions – more information to come for attendees.
  • Multi-dimentional imaging data will be made available for training purposes. Attendees are encouraged to submit/bring their own images and processing challenges.

The format will be introductory talks in the morning with five (5) hands-on stations that participants will rotate through in 75 minute intervals for the rest of the day. It is intended for imaging core directors and imaging scientists that are interested in the image processing and analysis pipelines in a shared environment. Participation is limited to 25 individuals.

Mark A. Sanders, Program Director of University Imaging Centers, University of Minnesota Lisa Cameron, Director, Light Microscopy Core Facility, Duke University and Duke University Medical Center

Station leaders:

Dr. Hamdah Shafqat Abbasi, Postdoctoral Associate, Carpenter Lab, Broad Institute of MIT and Harvard

CellProfiler is a free, open-source software, which allows to quantify numerous features from biological images. It has actively been by several research scientists for image-based assays and cited in more than 3,320 publications.

Resource Website(s): https://cellprofiler.org

Email Contact: imagingadmin@broadinstitute.org

Online Tutorials/Example images & pipelines:   https://cellprofiler.org/tutorials/



NIS Nikon Elements

Sally Miller, Bioscience Sales Specialist

Charles E Zogzas Ph.D., Advanced Biosystems Specialist

Nikon’s NIS-Elements Software is an integrated software imaging platform designed for both acquisition and analysis. It delivers comprehensive control of microscopes and peripheral devices, image capturing, , image analysis and data management. This system contributes to experiment efficiency with intuitive image analysis features and database building capabilities developed to archive and manage large numbers of multidimensional image files. Nikon’s software solution is powerful, easy-to-use, and customizable to meet the application requirements. With Nikon’s General Analysis Software Module, users can create custom, conditional/intelligent analysis workflows where the software automatically analyzes acquired images and dictates the next course of image acquisition based on the results. Nikon’s General Analysis module makes it possible for researchers to create their own custom image analysis routines. The system contributes to experiment efficiency with a database building feature (or database export) develop to handle archiving and searching of large numbers of multi-dimensional image files.



Molly McQuilken, PhD, Business Development Manager, Imaging – Southern US, Arivis Inc.

Arivis provides software for visualization, sharing, analysis and presentation of multi -channel 2D, 3D and 4D image data of almost unlimited size. One main product of the arivis platform, Vision4D is a modular software which provides users with the ability to handle hundreds of gigabytes or terabytes of 4D image data easily, as if they were a few megabytes in size. For quantification of this large image data the arivis analysis pipeline implemented in Vision4D offers a robust and flexible click-and-play solution for processing and quantification of any kind to allow users to extract important analytical information from their image files.



Rachel Finck, Senior Director of Informatics, Ionpath Inc.

Rachel will be presenting on IONpath's MIBI (Multiplexed Ion Beam Imaging) platform highlighting its web application, MIBItracker. The software addresses the data management and visualization challenges of highly multiplexed data, and seamlessly integrates with additional image analysis tools to provide end-users interactive access to view and share their data.

She will include a live demo of the application and how it fits into an image analysis pipeline in combination with open source tools. Users may also access sample data from MIBItracker linked from their website.



Bill Henderson, Sales/Applications Manager, ThermoFisher Inc.

Thermo Scientific Amira Software is a powerful, multifaceted 2D-5D platform for visualizing, manipulating, and understanding life science research data from many image modalities, including CT, MRI, 3D Microscopy, and other techniques.

The application enables advanced 3D/4D+ bioimaging workflows in research areas ranging from structural and cellular biology, to tissue imaging, neuroscience, preclinical imaging, and bioengineering. With a comprehensive array of tools for the flexible and accurate analysis of time series data of cellular processes, Amira enables researchers to perform dedicated segmentation workflows on their intra- and intercellular images and apply powerful automated object tracking solution. Amira aims at supporting researchers in the most frequently used image analysis techniques, such as filament tracing and editing, DTI analysis, brain perfusion analysis, and object tracking. Combining its versatility, with state-of-the-art 3D visualization and image processing, enables researchers to create custom workflows that extract exactly the desired type of information from an image.

Amira Software enables the fusion of any type of preclinical image data. Co-registered images can be segmented and analyzed using Amira Software’s vast library of image analysis filters and algorithms. Image segmentation and quantification workflows can be applied to entire time series of image data of dynamic processes. With Amira Software’s professional-grade visualization tools, structural information from CT and MRI can be augmented and rendered jointly with segmentation results and functional images to create visualization of physiological processes that reveal the underlying mechanisms in an intuitive animation.

Click here for registration information.

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Nikon Instruments

thermo fisher

Thermo Fisher Scientific