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 (email@example.com).
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:
Enter Images The storage locations and section numbers of the digitized images to be analyzed are specified and entered by Elegance into a database.
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.
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.
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.
Generate neuron diagrams From the data in the MySQL database, Elegance generates 1D or 2D neuron diagrams.
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:
Contex (Ontario, Canada) Cougar Tx 36 wide format scanner
Three Agfa (Ridgefield Park, NJ) Duoscan HiD scanners
Three image-processing Alienware (Miami, FL) workstations, each with a 2.2 GHz AMD Athlon 64 Fx-51 processor, 2 GB RAM, and an NVIDIA GeForce Fx5950 Ultra video card
Three Intel workstations each with a Pentium III processor and 2 GB RAM
A Linux-based server with 3.5 TB RAID 5 storage
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.