Reconstruction Software: Program Elegance

This laboratory has developed custom software for computer assistance in reconstructing neuron architecture and connectivity from serial section electron micrographs.  This software is available upon request.  Please contact Meng Xu (mxu@aecom.yu.edu).

Program Elegance

Our reconstruction software, termed Elegance, is a JAVA-based program that facilitates the handling of digitized images, the recording of features in the images, and the generation of neuron diagrams from information stored in a MySQL database.  The program is not C. elegans specific, and may be applied to any series of images of sectioned material where it is desired to connect points assigned to structures through a series of sections.

Reconstruction of a neuron using Elegance proceeds through the following stages:

  1. Enter Images  The storage locations and section numbers of the digitized images to be analyzed are specified and entered by Elegance into a database.

  2. Load Images  The images are brought to the screen individually or in groups.  Elegance provides for rotation, zoom, brightness control, and contrast control.  These properties are retained in overlays, leaving the original image data inviolate.

  3. Mark Profiles  On each image, the mouse is clicked in the center of the cross-section profile of the neuron of interest, as well as in the profiles of those neurons with which the neuron of interest interacts.  Elegance uniquely names each point (profile) and enters its X,Y, Z (section number) coordinates into a MySQL database.  Elegance displays each point in an overlay over the image.

  4. Enter Relationships  The experimenter specifies relationships between the points (profiles), using the mouse.  Relationships are entered into the MySQL database.  Relationships are of two types: continuity relationships and synaptic relationships
        Continuity specifies the relationship that exists between two profiles that are part of the same cell.  Profiles that are related by continuity typically are in adjacent sections.  Elegance accumulates all profiles in continuity relationship with each other into contins, partially-assembled intermediates analogous to contigs in DNA sequencing projects.  As parts of a single neuron, either branches or segments running through different regions, are connected, Elegance joins them together until the reconstructed neuron is represented by a single contin.
        Synaptic relationships occur between profiles within the same section.  Elegance can record pre- and post-synaptic cells at single and multiple chemical synapses and gap junction synapses.
        Once specified, continuity and synaptic relationships are shown on the screen in overlays so the experimenter can follow the data that has been entered.

  5. Generate neuron diagrams  From the data in the MySQL database, Elegance generates 1D or 2D neuron diagrams.

Hardware requirements

Elegance runs on standard, Windows-based PC hardware.  Our images are each 40 mb TIFF files.  We mark hundreds of profiles on each of thousands of images.  Our current hardware includes:

The server, accessed over a gigabit network, stores all our digitized images and the MySQL database.  Elegance is run on the three Alienware workstations.  The other workstations are used for scanning.