Java Advanced Imaging -- National Center for Microscopy and Imaging Research


Automated Mosaicking, Tomographic Dataset Reconstruction, and Remote Collaborative Telemicroscopy

The National Center for Microscopy and Imaging Research (NCMIR) at the University of California San Diego (UCSD) develops state-of-the-art 3D imaging and analysis technologies to help biomedical researchers understand biological structure and function relationships in cells and tissues. For more information, please visit

ImageJ Mosaic plugins

We have developed an automated mosaic acquisition and processing solution around the integration of a Nanomotion® -II motorized stage (Applied Precision LLC) and a Bio-Rad RTS 2000 2-photon confocal microscope. The processing involved in aligning and assembling the individually acquired images into a mosaic was developed using the ImageJ plugin framework with the core of the processing routines implemented using the JAI libraries. Navigation of the assembled mosaics was implemented with the JAI and the JadeDisplay libraries. Without JAI's paradigm of processing images in the form of discrete tiles, the assembling of the thousands of images involved in creating a mosaic would be inefficient if not impossible. By utilizing JAI's facilities, datasets of up to 60 gigabytes have been processed and future improvements are planned to push this limit even further.

Mosaic #1 Mosaic #2
(Click images for full-size.)


Jinx was developed to aid in the 3D reconstruction of tomographic datasets acquired with one of the various electron microscopes available at the resource. Tomographic datasets consist of a series of 2D images from which objects of interest are segmented out for the 3D reconstruction. Jinx offers the user a graphical interface to step through each image of the series and facilities to manually trace out objects of interest. It relies on JadeDisplay to support the display of large images with graphical overlays and the JAI libraries for histogram functionality and other types of image manipulations. Jinx is currently under active development and future releases will offer semi-automated segmentation algorithms based on fuzzy logic, level set, and watershed algorithms.

Jinx Screenshot
(Click image for full-size.)


The remote operation of the various electron microscope instruments available at the center has long been a focus of our engineering and software development. EMWorkspace is our most recent software effort to assist in remote and collaborative telemicroscopy sessions. It offers numerous tools for user collaboration, microscope control, image acquisition, and displaying of a live video stream during a session. To accommodate the different instruments, EMWorkspace dynamically changes the user interface to adjust for the functionalities offered by the different instruments. Future development of this software will include improvements to the live video subsystem and the integration of the Cell Centered Database (CCDB) for image storage.

EMWorkspace Screenshot
(Click image for full-size.)


Sunny Chow
George Yang
Mona Wong

Principal Investigator:

Mark Ellisman

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