Robert Pavlis, Girard, Kansas USA

Return to the author's Micscape article 'Microscope Digital Video Using Only Free Software'

There are a very large number of terms and acronyms associated with digital imaging and digital image processing. There are also some special ones involving imaging through microscopes and telescopes. This is a brief summary of some of these terms.

• Afocal projection This is a method of photography through optical instruments in which the image is obtained through the ocular of the instrument without removing the normal lens from the camera.
• BSD Berkeley Software Distribution. This is a POSIX type operating system developed at Berkeley. Earlier versions of it were often called Berkeley Unix. It is currently the basis for three free open source operating systems, freeBSD, openBSD, and netBSD. Computer users concerned about security often choose openBSD--it goal is to be the most secure operating system in existence. (Free operating systems generally are not certified as being compliant with standards even when they are eligible because of the substantial cost of registration and certification.)
• Colour temperature Digital colour images are normally stored by storing separate digital images in the three additive primary colours, red, green, and blue. The relative intensity of these three colours in a light source varies. Higher temperature light sources produce more blue and relatively less red. Standard tungsten filament lamps have a colour temperature of about 3000 degrees. This light is very red. Daylight is around 6000 degrees. It is much bluer. An imaging system utilising 3000 degree colour temperature must be much more sensitive to blue light than one utilising 6000 degree colour temperature light. The colour temperature of standard tungsten filament lamps varies as it is dimmed. This is one of the strongest reasons for converting microscope illumination to white light emitting diodes!! Digital cameras generally have a colour temperature adjustment, but one can adjust this manually with image editing software.
• CMYK Cyan, Magenta, Yellow, Key is a system for producing colour prints by subtractive colours with cyan, magenta, and yellow being the three primary subtractive colours. Key refers to black. Colour prints are made by putting subtractive dyes on paper or plastic stock. Cyan dyes remove red, magenta dyes remove green, and yellow dyes remove blue. Black dyes are often employed in colour printing because of imperfections in the three other dyes to force dark areas of the print to true black.
• Codec A codec is a computer system that can encode or decode digital data streams.
• Digital Zoom Digital Zoom is a polite way to describe cropping of digital images. For this reason it tends to result in poor images. It is a VERY poor substitute for optical Zoom.
• Eyepiece projection This is a method of photography in which an ocular is used to project an image directly onto the image plane of the camera with its lens removed. This technique can obviously only be used with cameras with removable lens. (Unless special oculars are used for this purpose serious aberrations are introduced by doing this.)
• Gamma Gamma encoding is used to code rgb values to map digital images (and analogue too) to make it seem more "even." Images with very bright and very dim areas need to be subjected to gamma correction or the bright areas will all appear white and the dim areas black. Monitors and television sets are designed for specific gamma corrected signals.
• GNU Gnu is Not Unix. The Free Software Foundation has used this term to describe their software licence system. The FSF original purpose was to develop a full scale free version of a POSIX operating system. This goal has been accomplished by the development of Linux, largely under their licence. The FSF licence has been applied to many programs that have no connexion to Unix type operating systems; however it is still encountered most often in Unix and Unix like operating system software.
• ieee 1394 This is a system for very high speed serial transfer of digital signals. Many digital video cameras use it to transfer data. When purchasing new digital video cameras, one should consider the lack of an ieee 1394 port as a very strong negative.
• JPEG Joint Photographic Experts Group. This is a "lossy" still image compression format. It dramatically compresses images over the level produced by separate bytes for red, green, and blue for each pixel. It does so at the cost of introducing serious artifacts. For this reason it should not be used for images of text. It is the most common method for transmitting images over the Internet. Most still digital cameras produce images in this format by default. PNG images are less compressed, but these artifacts are not introduced. (vide infra)
• Linux This was originally a kernel for a POSIX type operating system developed by Linus Torvalds. The term is now used to describe any full open source operating systems utilising this kernel. Some particularly notable examples include Debian, Fedora, Slackware, Suse, and Ubuntu.
• Magic number Because there are an extraordinarily large number of image and sound formats, there needs to be a way to mark data files for sound and images in some way. This is done by placing a "magic number" at the start of a file. Playback programs generally use the magic number to determine which codec to use.
• MPEG Moving Picture Experts Group. This is a large set of standards for digital video compression. There are several codecs associated with these standards.
• Ogg Ogg is a GNU container format for digital video and audio data. Ogg vorbis is an audio codec. Ogg theora is a video system.
• Open Source Proprietary computer programs are provided as an executable, non human readable, file or series of files. Open source programs are provided written in computer languages such as C, C++, FORTRAN, etc. A compiler program is necessary to convert these into executable programs. Many open source programs are provided with executable programs. The extreme advantage of open source programs is the simple fact that users with knowledge of computer languages can fix coding errors and recompile the program. Users can also compile the program for other computer operating systems, often with no modification.
• Optical Zoom A camera equipped with optical zoom has an objective with variable focal length. High quality zoom lenses produce excellent results. Digital zoom (see above) cannot compete by its very nature!
• PNG Portable Network Graphics. This is a system for compressing still digital images that does not lose information from the original uncompressed data. It is highly superior to JPEG for this reason. Its greater fidelity comes with the price of making the image files larger.
• PNM PNM refers to a series of image uncompressed image formats in which each point of the data file is directly mapped to the final image. PBM (Portable bitMap) maps bits to points, resulting in an image that is only black and white. (No grey!). PGM (portable grey map) maps numbers, usually bytes-0 to 255--to produce a grey image. PPM (Portable pixMap) maps three sets of numbers, usually bytes, the first for red, the next for green, the next for blue. PAM(Portable Anything Map) maps larger sets of numbers to produce images. Very large files are required for images coded this way. They are normally used for image editing and computer image manipulation. There is a set of routines called netpbm that can convert almost all existing image formats to and from these formats. When images are in odd image formats, more often than not netpbm has a routine to convert the image to one of the pnm formats, and it can be converted from there to a more common one. These formats are thus extremely important. Some scanners output images in ppm format. (Note: many image display programs are unable to display images that use more than 1 byte per colour, the pnm specification, however, allows two bytes per colour.)
• POSIX Portable Operating System Interface to UniX. This is basically a set of rules that describes how Unix type operating systems are supposed to behave. It exists to make it possible for computer users to use different POSIX compliant operating systems without retraining, and to facilitate migration of programs between operating systems that comply.
• Prime Focus Photography This is a technique for photography through instruments in which both the ocular and the camera lens are removed so that the instrument's objective projects an image directly on to the camera's image plane. With microscopes this technique tends to introduce serious aberrations.
• Quick Time Quick Time is a multi media system for digital sound and video that has been developed by Apple.
• rgb Red. Green. Blue. This describes a method of describing a digital image in terms of the three additive primary colours, red, green, and blue. Humans have three colour sensors in their eyes, so by combining these three colours in various proportions any colour can be simulated quite well. Colour monitors produce simultaneously red, green, and blue images that simulate (for humans) coloured objects very well.
• Root When a computer is running under Unix type operating system users must be logged in to the computer to use it. Each user must have an account and password to enforce security. Programs and files can only be accessed by a given user if that user be authorised to have such access. Root is the name given to a "super user" who can access and modify all of the computer's files. One should NEVER log in as root routinely because of the danger that comes with having such power! The password chosen for root should be a strong password to prevent unauthorised vandals from taking over the computer. The Unix type of security is the primary reason that computer vandals and criminals so seldom are able to attack computers so equipped.
• Shell In Unix type operating systems a shell is a text command processor. Computer users unfamiliar with Unix type operating systems often think of early microcomputer text command processors and shutter. Shells, however, have extraordinary power, and a single command can process thousands of files. Recently I needed to convert about 4000 files to smaller image formats so they would take up less space on a portable computer. I copied the original 4000 files to a single directory, and issued a single command that shrunk all 4000! (Users should beware! They can, in the hands of a careless user, create a computer disaster with such power! I know someone who was logged in as root and typed the shell command "rm -r / work/". The command should have been "rm -r /work/". But the / refers to the entire software installation--so the shell obediently deleted absolutely everything on the computer leaving no files at all.)
• sudo This is a Unix shell command that permits ordinary users to execute files that normally are only available to root. The user must be listed with the system as a "sudoer", and normally must provide his password before being allowed to execute the program. Computers are more secure if they lack a sudoer list. Sudo is different from the su shell command that allows ordinary users to log in to a new shell as root. Here the user must provide the root password.
• Unix Unix is the name originally given to a multi user multi tasking computer operating system designed by Bell Labs in the late 1960s. Today the trademark is owned by an industry standards group. Operating systems must be fully compliant with a set of specification to use the name.
• usb Universal Serial Bus is a system to connect devices to computers. The original system was rather slow, but usb-2 can transfer data and 480 megabits/second. Virtually all digital still cameras use this system. Some digital video cameras use this format exclusively, but higher quality ones have both usb and ieee 1394.
• Xvid Xvid is a video codec compliant with MPEG-4. It is a GNU licenced system. It produces excellent compression and good playback.
• Xwindow Xwindow is the original graphical user interface (GUI). It originated at MIT during the mid 1980s. It was originally designed for computer networks, and it is NOT a part of its host operating system. (Normally Unix and Unix like.) It also does NOT have an user interface program, this must be provided by a separate Window manager program. Different Window managers dramatically modify its "look and feel". X can run window managers from a remote computer. Because X is not part of the host operating systems it can "crash" without bringing down the host computer. A single computer can also execute multiple instances of X at once. Although many people view POSIX operating systems as being somewhat user hostile, X window managers now exist that are as simple to use as any computer systems ever devised. Although the X window system has been in existence for 25 years, many Window managers are of very recent origin.
• WMV Windows Media Video. This is a set of video codecs designed by Microsoft.