Jeffrey S. Prothero

Three-dimensional reconstruction from serial sections. IV. The reassembly problem

In many fields of biology and medicine there is a pressing need for quantitative descriptions of biological structures at a resolution of micrometers. This need is currently met best by three-dimensional reconstruction from serial sections. The preliminary steps in three-dimensional reconstruction include fixation, embedding in plastic, introduction of fiducials, serial sectioning, and staining. At the light microscope level, with which we are chiefly concerned, one will usually want to do photomicrography (or videomicrography) of adjacent fields within individual tissue sections. The resultant images are projected onto a digitizer pad and the contours of interest manually digitized. From the digitized coordinates generated thereby, one wishes to generate a likeness of the original object, using computer graphic displays, and to then do interactive morphometrics. The problem of combining the digitized coordinates so as to produce a numerically faithful representation of the original object (i.e., the reassembly problem) is, as a practical matter, nontrivial. A technical description of the reassembly problem is presented. The main factors entering into a solution of the problem are discussed and a mathematical statement of the solution is given.

Three-dimensional reconstruction from serial sections. I. A portable microcomputer-based software package in Fortran

Abstract A software package is described that is designed to simplify the collection, storage, and processing of data to be used for three-dimensional reconstruction from serial sections. The package, called MORPHO, consists of four independent programs, all written in FORTRAN, running under CP M , and called ISPY, DMPSPY, EDSPY, and STATSPY. The function of ISPY is to guide the user in the documentation, digitization, and storage of data derived from serial section images. The serial sections may be at any level of resolution: ultrastructural, microscopic, or macroscopic. DMPSPY allows the user to display and to make hard copies of the digitized contours. EDSPY allows any and all errors in data entry to be rectified simply and directly. STATSPY carries out statistical calculations, such as cross-sectional areas and volumes. A useful feature of STATSPY is the provision for easy insertion of additional subroutines to compute special statistics not currently provided.

Slisp: a flexible software toolkit for hybrid, embedded and distributed applications

JAMES F. BRINKLEY AND JEFFREY S. PROTHEROStructural Informatics Group, Digital Anatomist Program, Departmentof Biological Structure,Box 357420,University of Washington, Seattle, WA 98195, U.S.A. (email: brinkley@u.washington.edu,jsp@biostr.washington.edu)SUMMARYWe describe Slisp (pronounced ‘Ess-Lisp’), a hybrid Lisp–C programming toolkit for the development ofscriptable and distributed applications. Computationally expensive operations implemented as separateC-coded modules are selectively compiled into a small Xlisp interpreter, then called as Lisp functions in aLisp-codedprogram.The resulting hybrid programmay run in severalmodes: as a stand-alone executable,embedded in a different C program, as a networked server accessed from another Slisp client, or as anetworked server accessed from a C-coded client. Five years of experience with Slisp, as well experiencewith other scripting languages such as Tcl and Perl, are summarized. These experiences suggest that Slispwill be most useful for mid-sized applications in which the kinds of scripting and embeddability featuresprovidedby Tcl andPerl can be extendedin an efficient manner to larger applications, while maintaining awell-defined standard(Common Lisp) for these extensions.In addition, the generality of Lisp makes Lisp agood candidate for an application-level communication language in distributed environments.