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Downloads
At several meetings in the US and overseas, I have been asked to present a plenary lecture on the characteristics of our human visual system and how it interacts with the images that are obtained from various kinds of microscopy (and other scientific images). The basic message is that humans are not very good observers, that our vision system ignores a lot of information, that having names and labels for recognized features is very important, and that we often think we see what we expect to see. After the most recent presentation, urged on by several of the people at the conference, I have prepared a written version of the paper which was recently serialized in the Proceedings of the Royal Microscopy Society. It is about 25,000 words long, has more than 80 illustrations, and can be downloaded as a 6 MB Acrobat (pdf) file. In the presentation I include a few quicktime movies, which are shown in the pdf file as single still frames. This is probably sufficient for the reader to understand the message, but if anyone wants the actual 600K of *.mov files they can also be downloaded (Figures 23, 27, 35 and 36).
A 150 page tutorial showing step-by-step use of Photoshop and Fovea Pro has been entirely revised and rewritten for the most recent (version 4.0) release of the software by Reindeer Graphics. The entire tutorial can be accessed or downloaded on-line as a series of Acrobat (*.pdf) files.
At several recent workshops, students have inquired about using the Fovea Pro plugins with Photoshop CS3 on a current generation Macintosh computer (with an Intel processor). Click here for full information and access to updated plug-ins for use in this environment.
I am frequently asked to provide a brief (half-day) introductory session on Photoshop, before extended hands-on workshops on image processing and analysis. This is intended to help those unfamiliar with the Adobe Photoshop environment learn about the program's basic functions, general appearance, and those capabilities which it offers that are appropriate for scientific imaging. A 28-page tutorial can be downloaded as a 12MB Acrobat (*.pdf) file. A 2.5 MB zip file containing the images used in the tutorial is also provided. In response to a frequent request to show how a poster for a scientific session can be assembled, I have also prepared a 4-page step-by-step description.
Another common concern is the choice of a camera appropriate for use on a light microscope. I personally use a wide variety of cameras, ranging from specialized cameras intended for that application to general purpose digital cameras including single-lens-reflex models with adaptors, and even consumer cameras that look through the microsope eyepiece (which have the advantage of portability). Some of the factors to consider when choosing a camera are described in this brief writeup.
Lossy compression of images, most often using the JPEG algorithm, is simply unacceptable if they are to be used for scientific or forensic purposes. An article illustrates some of the types of artefacts that are caused, both in photographs and in thresholded binary images intended for measurement.
Whether images are being used for scientific or forensic purposes, it is vital to understand how processing affects the perception or measurement of the scene. The ethics of what constitutes proper methods for image processing is something that must be considered. My statement on this subject is available for download.
The Molecular Expressions web site hosted by Mike Davidson's group at Florida State University has an on-line set of my lecture notes enhanced by dozens of interactive Java applets, covering many of the topics that I present in a typical one-day tutorial.
Several brief tutorials showing several useful sequences of commands using Photoshop and Fovea Pro plug-ins can be also downloaded. These have several uses: 1) they produce useful results in many real circumstances; 2) the demonstrate the uses of the component functions and contribute to learning more about the available tools; and 3) they can be made into actions, which are an extremely powerful means for automating repetitive or complex operations.
Superimpose colored outlines around features on the original grey scale or color image.
Create a more effective rolling ball filter to remove dust and other small artefacts from an image.
Generate a surface image with contour lines from a range image (e.g., from an AFM).
Merge and align three images to form a color composite (may be useful for images acquired through different colored filters, or using different imaging modes in an AFM, or different accelerating voltages or detectors in an SEM, for example).
For further info: