Montage Serial Reconstruction System

This page is intended to provide information about Montage, a serial-reconstruction package that allows a user to reconstruct serial data in 3 dimensions on a relatively inexpeisive PC.

On-beta ganglion cell by Ethan Cohen.

For more examples, check out our database of reconstructed cells.

Features:

It's free (source code included)
Runs under Linux, a free unix-like OS for the PC
Requires little specialized hardware (only a bitpad)
Comes with several programs for analyzing and displaying the data
Manual comes with distribution.

Capabilities:

Multiple data types:
- trace (open or closed polygonal contour)
- base (reference point)
- flag (can be displayed as a circle, triangle, rectangle)
- line
- grain
Multiple data specifications: cell, branch, color
User-definable section buffer size at run-time
Multiple output formats:
- SVGA
- X-Windows
- PostScript (color and grayscale)
- HP plotter
True 3-d visualization schemes in development (see below)

Availability

retina.anatomy.upenn.edu/pub/mont.linux.tgz

here

Montage is one of the first serial reconstruction packages, and it remains one of the best. It was originally written for a Z80 system with floating-point hardware, and has since been ported to Venix, and most recently, Linux. The digitization program runs best in Linux's SVGA mode, and the display program is normally run under XWindows. The entire source compiles with GCC which ensures portability.

3-d visualization schemes

For true 3-d visualization, there are currently two systems in development. One is Tom Chou's contour picker and surface tiler, which produces a surface composed of triangles for AVS's geometry viewer. The source code for this method is available by request.

The other, Nuages, is in the initial stages of investigation. Nuages is Bernhard Geiger's package (ftp://betelgeuse.inria.fr/pub/Nuages/NUAGES-*.tar.Z). Generally, it seems to produce nice output in any one of a number of formats: .off (Geomview's object file format), .obj (wavefront format, easily converted to AVS .geom), .vera (vera raytracer format, convertable to POV-Ray format), as well as a few others. Nuages also has the added feature of outputting surface normals for the triangles, making for smoother final images.

Comments, questions, requests, etc., should be emailed to "rob@retina.anatomy.upenn.edu". -Rob