Computer Graphics in Biology, Softcover reprint of the original 1st ed. 1986
Computers in Biology Series

Computer graphics is being used to an increasing extent in the biological disciplines. As hardware costs drop and technological developments intro­ duce new graphics possibilities, researchers and teachers alike are becoming aware of the value of visual display methods. In this book we introduce the basics of computer graphics from the standpoints of both hardware and software, and review the main areas within biology to which computer graphics have been applied. The com­ puter graphics literature is vast, and we have not been able to give a full course on graphics techniques in these pages. We have instead tried to give a fairly balanced account of the use of graphics in biology, suitable for the reader with some elementary grounding in computer programming. We have included extensive references both to material cited in the text and to other relevant publications. One of the factors that has fuelled the increase in graphics use is the ease with which the more simple graphics techniques may be implemented on microcomputers. We hav.e, therefore, paid attention to microcomputer graphics as well as graphics techniques suitable for larger machines. Our examples range from simple two-dimensional graph plots to highly complex surface representations of molecules that require sophisticated graphics devices and mainframe computers on which to run. The book is separated into two logical sections. The first part con­ centrates on general graphics techniques, giving an overview from which the reader will be able to refer to other more specialised texts as required.

1. An Introduction to Computer Graphics.- 1.1 The beginnings of computer graphics.- 1.2 What is computer graphics?.- 1.3 Computer graphics and biology.- 1.4 The elements of a computer graphics system.- 1.5 Computer graphics in perspective.- 1.6 References.- 2. Graphics Hardware.- 2.1 An overview.- 2.2 Input devices.- 2.3 Display devices.- 2.4 Display processors.- 2.5 The computer.- 2.6 References and bibliography.- 3. Graphics Software.- 3.1 Connecting computers and graphic devices.- 3.2 Graphics software packages.- 3.3 Graphics packages on mini computers and mainframe computers.- 3.4 Microcomputer graphics software.- 3.5 Graphics workstations.- 3.6 The applications program.- 3.7 References and bibliography.- 4. Two-dimensional Graphics.- 4.1 The elements of two-dimensional transformations.- 4.2 Representation of points.- 4.3 Straight line transformations.- 4.4 Rotation.- 4.5 Reflection.- 4.6 Multi-operation transformations (composition).- 4.7 Two-dimensional homogeneous coordinates.- 4.8 Two-dimensional rotation about an arbitrary axis.- 4.9 References.- 5. Three-dimensional Graphics.- 5.1 Basic concepts.- 5.2 Three-dimensional homogeneous coordinates.- 5.3 Three-dimensional scaling.- 5.4 Three-dimensional shearing.- 5.5 Three-dimensional rotations.- 5.6 Reflection in three dimensions.- 5.7 Three-dimensional translation.- 5.8 Three-dimensional rotation about an arbitrary axis.- 5.9 Projections.- 5.10 Conclusions.- 5.11 References.- 6. Hidden Lines and Hidden Surfaces.- 6.1 An introduction to hidden lines and surfaces.- 6.2 A simple hidden lines algorithm.- 6.3 The Galimberti and Montanari algorithm.- 6.4 The hidden surface problem.- 6.5 A preliminary classification.- 6.6 Surface representation and hidden surface methods.- 6.7 Conclusions.- 6.8 References and bibliography.- 7. Graphical Representation of Biological Data.- 7.1 Introduction.- 7.2 Graphs and histograms.- 7.3 Point plots and transforms.- 7.4 Graphics data structures.- 7.5 A data structure for hidden lines treatment.- 7.6 References.- 8. Reconstruction Methods for Cell Systems.- 8.1 Tissue reconstruction.- 8.2 The role of computer graphics.- 8.3 Input of data.- 8.4 Two-dimensional analyses.- 8.5 Three-dimensional reconstruction.- 8.6 Three-dimensional reconstruction of neurones (CELL).- 8.7 Three-dimensional reconstruction of non-neural tissue (RECON).- 8.8 Other three-dimensional reconstruction programs.- 8.9 References and bibliography.- 9. Image Capture and Image Analysis.- 9.1 Biological images.- 9.2 Image capture devices.- 9.3 Analysis of periodic images.- 9.4 The Joyce-Loebl Magiscan.- 9.5 Reconstruction from X-ray data.- 9.6 References and bibliography.- 10. Molecular Graphics.- 10.1 An introduction to molecular graphics.- 10.2 Components of a molecular graphics system.- 10.3 Molecular data.- 10.4 Examples of molecular graphics packages.- 10.5 Some existing systems.- 10.6 References and bibliography.- 11. Simulation and Animation.- 11.1 Moving pictures.- 11.2 Hardware for real-time animations.- 11.3 Concepts of graphic animation.- 11.4 Dynamic graph construction.- 11.5 Simulation of cell division and cell interaction processes.- 11.6 Animation of genetic events.- 11.7 References and bibliography.- Appendix 1: Matrix Manipulations.- A1.1 Basic definitions.- A1.2 Vectors.- A1.3 Matrix addition.- A1.4 The trace of a matrix.- A1.5 The determinants of a matrix.- A1.6 Multiplication by a scalar.- A1.7 Matrix multiplication.- A1.8 References.- Appendix 2: A Graphics Glossary.