Scientific Imaging with Photoshop: Methods, Measurement, and Output by Jerry Sedgewick

Book Description

Adobe Photoshop is one of the more powerful tools available to scientists today. It is indispensable in the preparation of digital images of specimens for measurement, especially for separating relevant features from background detail. Scientific Imaging with Photoshop is the authoritative guide to the use of Photoshop in scientific research, with a special emphasis on the ethical ramifications of the use of image-enhancement software to extract data from digital images. Beginning Photoshop users will benefit from its tutorials in the basics of image processing, and more sophisticated users will appreciate the sections on automating Photoshop operations with actions. In addition, the book lays out procedures in straightforward language for acquiring digital images as well as outputting processed images in digital and hard-copy formats.

Scientific Imaging with Photoshop provides all this and more:
• Little-known methods separating features of interest from the background for subsequent quantification
• How to make dense colors and subtle visual detail reproduce properly in publication
• Correct Photoshop methods and techniques for all user levels
• Procedures that are usable in legacy versions of Photoshop as well as Photoshop Elements and Photoshop Extended

Jerry Sedgewick has been the director for the Biomedical Image Processing Lab at the University of Minnesota for over 10 years. The lab is a light microscopy core facility serving scientists and engineers at the University and in local industry. Jerry works side-by-side with members of the research community on a daily basis.  He has co-authored articles in numerous publications, including Science (for which he has created two covers) and Circulation, and he is the author of Quick Photoshop for Research: A Guide to Digital Imaging for Photoshop 5x, 6x and 7x.

Product Details

Source: Science News
Written by Julie J. Rehmeyer

“Coral Star” shows the motion brought about by one particular dynamical system.
By Michael Field

Mathematicians often rhapsodize about the austere elegance of a well-wrought proof. But math also has a simpler sort of beauty that is perhaps easier to appreciate: It can be used to create objects that are just plain pretty—and fascinating to boot.

That beauty was richly on display at an exhibition of mathematical art at the Joint Mathematics Meetings in San Diego in January, where more than 40 artists showed their creations.

Michael Field, a mathematics professor at the University of Houston, finds artistic inspiration in his work on dynamical systems. A mathematical dynamical system is just any rule that determines how a point moves around a plane. Field uses an equation that takes any point on a piece of paper and moves it to a different spot. Field repeats this process over and over again—around 5 billion times—and keeps track of how often each pixel-sized spot in the plane gets landed on. The more often a pixel gets hit, the deeper the shade Field colors it.

The reason mathematicians are so fascinated by dynamical systems is that very simple equations can produce very complicated behavior. Field has found that such complex behavior can create some beautiful images. For example, the dynamical system he depicts in “Coral Star” does some peculiar things as it gets closer to the center (technically, the equation is discontinuous at the origin). So as you get closer and closer to the center, the image gets more and more complex.

“Even apart from the center, the image has quite a lot of depth to it,” Field says. “It’s a feature of the way it’s colored. I’m not so keen on bright primary colors. The shading makes it more interesting.”

This image has an unusual 35-fold symmetry, and Field created it as a present for his wife on their 35th anniversary.

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The website for the exhibition is at www.bridgesmathart.org/art-exhibits/jmm08/.

Copies of the catalogue for the exhibit, complete with high-quality reproductions of all the pieces of art, are for sale at www.mathartfun.com.

METACOW: A Public-Domain, HighResolution, Fully-Digital, Noise-Free, Metameric, Extended-Dynamic-Range, Spectral Test Target for Imaging System Analysis and Simulation

Geek Alert: the following would really only excite a “color geek”…

Sent in from Greg Barnett of RIT is this info about a geeky color test target from the Munsell Color Science Lab at RIT (that’s Rochester Institute of Technology for those who didn’t attend school there). From the web site:

“Standard, easily accessible, test targets have long served the field of color imaging as a foundation for comparison of the performance of various imaging systems and algorithms and the open and meaningful exchange of research results. This website details the creation and application of a new digital color test target useful for research and development of color imaging systems. The target has several advantages over previous types of targets that include spatial resolution, dynamic range, spectral resolution, metameric properties, lack of noise, and continuous tonal variations. All these features can be important for visual assessment, computational analysis, and colorimetric evaluation. This target, known as METACOW, is freely available to all performing research in color imaging.”

The METACOW test target is available to all for use in imaging system design and evaluation. Since it is such a large image it is not really practical to download, it will be provided on DVD for a nominal $25 media & shipping/handling fee. On this fabulous DVD you get: Many Gigs of Fullsize METACOW Glory, Smaller and Easier to Manage MINIMETACOW, Matlab Source Code for Reading and Rendering METACOW, and Much More.

Or you can download a smaller version (420×600x77) here: Small METACOW Images.

Contact Garrett Johnson or Mark Fairchild for details on how to order your very own METACOW DVD

A little-known field of ophthalmology soon will get work space in Ann Arbor that matches the stature a University of Michigan team has achieved.

A $1.5-million grant awarded in October by the Harry A. and Margaret D. Townsley Foundation will help U-M build a state-of-the-art Ophthalmic Imaging Center in the new Kellogg Eye Center under construction.

Scheduled to open in 2010, it will house six camera rooms, a photo studio, a waiting area and a larger work space.

When ophthalmologists review milestones in their field, they will likely credit Richard Hackel, chief of the U-M ophthalmic photography program, as the person whose digital images helped transform the diagnosis of eye disease.

In 1995, Hackel changed an arduous process of cutting and pasting together dozens of photos of the eye’s interior — much the way a collage is made — into digital photographs that precisely capture its texture and color.

Today, ophthalmic photography is an important adjunct to the diagnosis of eye disease. It also is used to monitor whether patients benefit from certain treatments.

In that way, a computerized photo can spare patients from undergoing possibly risky, invasive procedures and save money by avoiding unnecessary treatments that may cost $2,000 or more.

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Source: Chemistry World
Written by John Bonner

Researchers in the US have developed a technique that could allow neurologists to draw a detailed wiring plan of the mammalian brain by inserting genes coding for fluorescent proteins into mice. Dubbed ‘Brainbow’, the system reveals individual neurons within the nervous system in up to 90 different colours.

The work by Jeff Lichtman and colleagues in the Department of Molecular and Cell Biology at Harvard University uses a combination of genes from natural sources such as bioluminescent jellyfish or corals and man-made constructs to produce proteins in four different ‘primary’ colours, red, yellow, cyan and orange. The researchers inserted the genes into the mice genome using the Cre/Lox recombination method developed by Du Pont in the 1980s. This allows tissue specific modification – in this case, the genes are expressed only in the cells of the central nervous system.

One or more gene constructs may be present in a single cell and the entirely random expression of these proteins in the cell cytoplasm creates the many possible colour combinations.

‘In some cells we see a greyish colour because all the proteins are expressed about equally. But in most cells the proteins are at different concentrations giving us a range of hues,’ Lichtman told Chemistry World.

The group has been using the system to investigate the changes in the neural circuitry that occur during early development and have tracked the changes that occur in the mouse brain over the first 50 days.

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Digital imaging technology has been used in forensics since at least 1992, yet until now there has been no practical instruction available to address the unique issues of image processing in an everyday forensic environment.

Photoshop CS3 for Forensics Professionals: A Complete Digital Imaging Course for Investigators
George Reis
ISBN: 978-0-470-11454-4
Published by Sybex
Paperback
252 pages
July 2007
List price: $59.99
Amazon price: $37.70

The world locked eyes with a suspected pedophile today after a lot of digital photo manipulation and an apparently unprecedented global appeal by Interpol to help find him. From Agence France-Presse:

“For years, images of this man sexually abusing children have been circulating on the Internet,” Interpol chief Ronald Noble said in a statement.

“We have tried all other means to identify and to bring him to justice, but we are now convinced that without the public’s help this sexual predator could continue to rape and sexually abuse young children whose ages appear to range from six to early teens.”

This was “the first time the organization has made such an appeal,” Interpol stressed.

The suspect wasn’t caught in the act so much as found performing with a mask in public. About 200 photos of the suspect with 12 different young boys were located on the Internet in December 2004, an Interpol official said. But in each image, his face was obscured, apparently by use of a standard Adobe Photoshop effect called twirl, which is used by digital artists to manipulate images.

Apparently, the suspect, or whoever handled the pictures, did not think it was possible to reverse the twirling, a capability that at least one Interpol official was intent on keeping confidential.

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PHOTOGRAPHY: FIRST PLACE (TIE)
What Lies Behind Our Nose?
Kai-hung Fung,*

Source: Science Magazine

Written by Jeff Nesbit, Director, Office of Legislative and Public Affairs, NSF
Monica Bradford, Executive Editor, Science

Scientific data are the currency of science, but they often buy little understanding outside science itself–or even outside the narrow confines of a single scientific discipline. But when data are brought to life through images, illustrations, computer graphics, and animations, they can stimulate excitement, awe, new ways of looking at things, and, above all, a broad appreciation of even the most esoteric scientific information.

For the past 5 years, Science and the National Science Foundation (NSF) have cosponsored annual challenges to encourage cutting-edge efforts to visualize scientific data. Our interest in supporting these competitions is based on our firm belief that bringing data to life visually will be increasingly important not only for public understanding of science and engineering but also for improving communication across scientific disciplines.

This year, we received more than 200 entries from 34 states and 23 countries representing every continent except Antarctica. A committee of staff members from Science and NSF screened the entries, and an outside panel of experts in scientific visualization reviewed the finalists and selected the winners. (No awards were made this year for illustration.)

We encourage you to submit applications for next year’s challenge, details of which will be available at www.nsf.gov/news/special_reports/scivis/index.jsp, and to join us in celebrating this year’s winners.

Susan Mason of NSF organized this year’s challenge. Benjamin Lester of Science’s news staff wrote the text that accompanies the images in this special section, and Stewart Wills and Tara Marathe put together a special Web presentation at www.sciencemag.org/sciext/vis2007.

]]> http://photoshopnews.com/2007/10/03/2007-visualization-challenge-winners/feed/ 0 http://photoshopnews.com/2007/04/11/eye-diseases-gave-great-painters-different-vision-of-their-work/ http://photoshopnews.com/2007/04/11/eye-diseases-gave-great-painters-different-vision-of-their-work/#comments Wed, 11 Apr 2007 17:37:15 +0000 PSN Editorial Staff http://photoshopnews.com/2007/04/11/eye-diseases-gave-great-painters-different-vision-of-their-work/ Source: PhysOrg.com

Michael Marmor, MD, wanted to know what it was like to see through the eyes of an artist. Literally.

After writing two books on the topic of artists and eye disease, the Stanford University School of Medicine ophthalmologist decided to go one step further and create images that would show how artists with eye disease actually saw their world and their canvases.

Combining computer simulation with his own medical knowledge, Marmor has recreated images of some of the masterpieces of the French impressionistic painters Claude Monet and Edgar Degas who continued to work while they struggled with cataracts and retinal disease.

The results are striking.

In Marmor’s simulated versions of how the painters would most likely have seen their work, Degas’ later paintings of nude bathers become so blurry it’s difficult to see any of the artist’s brush strokes. Monet’s later paintings of the lily pond and the Japanese bridge at Giverny, when adjusted to reflect the typical symptoms of cataracts, appear dark and muddied. The artist’s signature vibrant colors are muted, replaced by browns and yellows.

“These simulations may lead one to question whether the artists intended these late works to look exactly as they do,” said Marmor who has long had interest in both the mechanics of vision and the vision of artists. “The fact is that these artists weren’t painting in this manner totally for artistic reasons.”

Degas and Monet were both founders of the Impressionist era, and their artistic styles were well formed before their eye disease affected their vision. But their paintings grew significantly more abstract in later life as, coincidentally, their eye problems increased.

“Contemporaries of both have noted that their late works were strangely coarse or garish and seemed out of character to the finer works that these artists had produced over the years,” Marmor wrote in a paper titled “Ophthalmology and Art: Simulation of Monet’s Cataracts and Degas’ Retinal Disease” that was published in the December issue of the Archives of Ophthalmology.

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]]> http://photoshopnews.com/2007/04/11/eye-diseases-gave-great-painters-different-vision-of-their-work/feed/ 0 http://photoshopnews.com/2006/12/04/jackson-pollocks-art-and-fractal-analysis/ http://photoshopnews.com/2006/12/04/jackson-pollocks-art-and-fractal-analysis/#comments Mon, 04 Dec 2006 17:27:49 +0000 PSN Editorial Staff http://photoshopnews.com/2006/12/04/jackson-pollocks-art-and-fractal-analysis/

Can mathematics explain the art of Jackson Pollock? Can it be used to authenticate paintings of uncertain provenance? Case Western Reserve University physicists address these questions in the current issue of Nature.
Source: Physorg

Case physics doctoral student Katherine Jones-Smith first encountered these questions in December 2004 when preparing for a weekly astrophysics seminar. Jones-Smith performed a Google search that linked her to research by University of Oregon physicist Richard Taylor and collaborators, who claim that Jackson Pollock’s famous drip paintings, are fractals. Fractals are complex geometric shapes that have been studied by mathematicians since the 1970s.

In articles that appeared in scientific journals and news magazines including Nature, Physics World and Scientific American, Taylor and coworkers also claim that fractal analysis can be used to distinguish Pollock’s drip paintings from imitations.

Intrigued, Jones-Smith began to examine Taylor’s articles, but quickly found that the work was seriously flawed. She showed that doodles that she could make in minutes using Adobe Photoshop were as fractal as any Pollock drip painting, vividly refuting Taylor’s claim that Pollock was able to generate fractals by hand only because he had attained a mastery of chaotic motion.

Jones-Smith presented a pointed critique of Taylor’s work to Case astrophysicists and was encouraged to write up her critique for publication. But since Taylor’s original work had appeared in Nature five years earlier, she thought interest in the topic had waned.

That changed this February when Taylor was invited by the Pollock-Krasner Foundation to determine the authenticity of paintings recently found by Alex Matter, son of the late photographer Herbert Matter. According to Matter, a close personal friend of Pollock’s, the paintings are the work of Pollock, but Taylor used fractal analysis to pronounce them inauthentic.

Convinced now that her work might still be of interest, Jones-Smith developed her critique into the article, Revisiting Pollock’s Drip Paintings, co-authored with Harsh Mathur, Case professor of physics.

“Untitled 5,” the drawing used by Katherine Jones-Smith and Richard P. Taylor for the fractal study.

A key element of the paper is a painting called Untitled 5 that Jones-Smith created in a matter of minutes in Photoshop. Untitled 5 depicts a field of stars and looks like the kind of drawing the proud mother of a three-year old might stick on a refrigerator door, says Jones-Smith. But, according to the fractal authentication criteria that Taylor has made public, it is an authentic Pollock.

Jones-Smith adds, “I found I can make paintings at will in Photoshop that meet all the criteria he has made public.”

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Additional article in The New York Times
(free registration required)

]]> http://photoshopnews.com/2006/12/04/jackson-pollocks-art-and-fractal-analysis/feed/ 0 http://photoshopnews.com/2006/11/20/imaging-technology-restores-700-year-old-sacred-hindu-text/ http://photoshopnews.com/2006/11/20/imaging-technology-restores-700-year-old-sacred-hindu-text/#comments Mon, 20 Nov 2006 18:18:35 +0000 PSN Editorial Staff http://photoshopnews.com/2006/11/20/imaging-technology-restores-700-year-old-sacred-hindu-text/
Scientists who worked on the Archimedes Palimpsest are using modern imaging technologies to digitally restore a 700-year-old palm-leaf manuscript containing the essence of Hindu philosophy.

The project led by P.R. Mukund and Roger Easton, professors at Rochester Institute of Technology, will digitally preserve the original Hindu writings known as the Sarvamoola granthas attributed to scholar Shri Madvacharya (1238-1317). The collection of 36 works contains commentaries written in Sanskrit on sacred Hindu scriptures and conveys the scholar’s Dvaita philosophy of the meaning of life and the role of God.

The document is difficult to handle and to read, the result of centuries of inappropriate storage techniques, botched preservation efforts and degradation due to improper handling. Each leaf of the manuscript measures 26 inches long and two inches wide, and is bound together with braided cord threaded through two holes. Heavy wooden covers sandwich the 340 palm leaves, cracked and chipped at the edges. Time and a misguided application of oil have aged the palm leaves dark brown, obscuring the Sanskrit writings.

“It is literally crumbling to dust,” says Mukund, the Gleason Professor of Electrical Engineering at RIT.

According to Mukund, 15 percent of the manuscript is missing.

“The book will never be opened again unless there is a compelling reason to do so,” Mukund says. “Because every time they do, they lose some. After this, there won’t be a need to open the book.”

Mukund first became involved with the project when his spiritual teacher in India brought the problem to his attention and urged him to find a solution. This became a personal goal for Mukund, who studies and teaches Hindu philosophy or “our way of life” and understood the importance of preserving the document for future scholars. The accuracy of existing printed copies of the Sarvamoola granthas is unknown.

Mukund sought the expertise of RIT colleague Easton, who imaged the Dead Sea Scrolls and is currently working on the Archimedes Palimpsest. Easton, a professor at RIT’s Chester F. Carlson Center for Imaging Science, brought in Keith Knox, an imaging senior scientist at Boeing LTS, as a consultant. Mukund added Ajay Pasupuleti, a doctoral candidate in microsystems at RIT, and the team was formed.

The scientists traveled to India in December 2005 to assess the document stored at a monastery-like mathas in Udupi, India. Sponsored by a grant from RIT, the team returned to the monastery in June and spent six days imaging the document using a scientific digital camera and an infrared filter to enhance the contrast between the ink and the palm leaf. Images of each palm leaf, back and front, were captured in eight to 10 sections, processed and digitally stitched together. The scientists ran the 7,900 total images through various image-processing algorithms using Adobe Photoshop and Knox’s own custom software.

Image A

Image B

Each palm leaf of the sacred Hindu manuscript, the Sarvamoola granthas, was captured in multiple sections, processed and digitally stitched together. Image A shows the condition of an original leaf from the text, stitched together but unprocessed. Image B shows a stitched and processed page after applying modern imaging technologies. Images were taken by Roger Easton, from Rochester Institute of Technology, and Keith Knox, from Boeing LTS, using a Sensys scientific digital camera and an infrared filter.

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Original information source: Rochester Institute of Technology

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