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From Image Tiles to Web-Based Interactive Measurements in One Stop

Antoine Vandecreme , 1 Michael Majurski , 1 Joe Chalfoun , 1 Keana Scott , 2 John Henry J. Scott , 2

Mary Brady , 1 and Peter Bajcsy 1 * 1 Information Technology Laboratory , National Institute of Standards and Technology , Gaithersburg , MD 2 Material Measurement Laboratory , National Institute of Standards and Technology , Gaithersburg , MD


Abstract : This article introduces readers to a web-based solution useful for interactive nanoscale measurements of centimeter-sized specimens. This solution is a client-server system that promotes collab- orative measurements and discovery. The system consists of multiple computational modules that enable uploading microscopy images, extracting metadata, assembling many nanometer-resolution images into an image covering a centimeter-sized area, and interactive viewing and measuring of objects of interest at multiple length scales over terabyte-sized images. We illustrate the use of the system on images of aerosolized nanoparticles and dye particles on printing paper.


Modern imaging technology has enabled nanoscale imaging to become a routine process. As imaging technology improves and image size increases, application measurement needs become more demanding and complex. These needs can be illustrated in the application areas such as nanoparticle detection during a manufacturing process or dye particle characterization in printing processes. For example, nanoparticles released during manufacturing processes can impact worker safety, and the number, size, morphology, and distribution of the released particles can help in better assessing the hazards associated with these processes and minimizing the risk to workers. In printing processes, fi nal dye particle size and distribution in the coatings layer or paper fi bers can vary depending on the environmental conditions. Although we are able to image nanoscale features and phenomena with relative ease, application-specifi c measure- ments such as nanoparticle morphology or dye particle size distribution over large physical scales are non-trivial because of the complex computations and associated require- ments imposed on both soſt ware and hardware. If such measurements are made possible, scientists could gain a better understanding of how nanoscale features are spatially distributed and how they interact with macro and mesoscopic scale environments. Several advanced microscopes have the capability to automatically acquire overlapping images of small fields of view [ 1 – 2 ]. This capability provides a way to image a large fi eld of view (FOV) of a centimeter-sized specimen and then take measure- ments at multiple physical length scales. However, automated specimen scanning yields thousands of small FOVs (or image tiles) that need to be


pre-processed into one large FOV, visualized during explora- tions, and measured to extract useful information. The large FOV is typically of the order of giga-pixels. A set of large FOVs over time, across wavelengths, or with varying z -dimensions can reach terabyte (TB) storage levels. T ese TB-sized 3D data sets pose challenges to on-the-fly measurement, interactive exploration, and collaborative discovery. In other words, while it is possible to collect the necessary images at the requisite resolution, it is hard to examine these images as a whole and interpret the data collaboratively to understand the physical phenomena under study.

This article introduces a web-based system that enables a user to explore and measure objects of interest at multiple length scales interactively and collaboratively aſt er thousands of small FOVs are pre-processed into a set of large FOV images. We illustrate the use of the system on gigapixel images of aerosolized nanoparticles and dye particles on printing paper. Other larger data sets that have been processed using the systems are available at

Materials and Methods Electron microscopy test data . We imaged a specimen

of nanofi bers air sampled onto a Si wafer using an FEI Helios NanoLab 650 + (Hillsboro, OR) focused ion beam scanning electron microscope (FIB SEM). Small FOVs of a specimen were acquired and stored as TIFF images using FEI’s MAPS correlative microscopy software. The small FOVs overlap by 10% in horizontal and vertical directions and form a grid

Figure 1 : Overview of the data and analysis workfl ows showing the possible interactions by multiple users. First, a user uploads images via his browser and specifi es parameters for assembling collections of small FOVs into one large FOV. The assembly consists of a minimum of three steps, such as tile stitching, intensity scaling to 8 bits per pixel, and pyramid building. Next, a user confi gures his views of multiple channels (overlays of multiple pyramids) and multiple time points (pyramid sequences), and then takes intensity measurements via interactive display, distance measurements using a scale bar or two-point mouse clicks, and object count measurements by running fi ltering and connectivity analysis tools in a browser.

doi: 10.1017/S1551929516000912 • 2017 January

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