Join Eric Wexler for an in-depth discussion in this video Understanding imaging in biomedical research, part of Photoshop CS3 Extended for BioMedical Research.
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Imaging makes up a substantial part of biomedical research. The number of pictures you see and subject matter which relies on imaging has grown and shows no signs that the increase will slow. If anything, with easier access to digital imaging systems and development of even more complex and target instrumentation, a scientist's reliance on imaging will only become more important. Here are just a few magazine covers I had lying around, and you can see how in each one of them imaging plays an important role in communicating what's happening in the scientific field.
Understanding imaging will help scientists improve their research. Of course to understand imaging is to realize the fundamentals of biological vision and digital imaging, the ways that each work and how they interact, the pros and cons of each different system. In the next few videos we are going to talk about the imaging systems, whether biological or electronic. We are going to talk about some acquisition, processing, storage output, and perception of seeing. This is a conceptual overview and for a more in depth understanding, there are multitude of books, courses, and experts on the subject.
First, we are going to look at acquisition systems. These are the sources of research images. The eye camera scanner, gel readers, medical imaging equipment like X rays. When you look at imaging equipment in science and types of instruments, they go well beyond just consumer cameras and scanners. Biomedical research imaging equipment can fit in four families. There is the microscope family. The microscope must be coupled with a sensor of some type. For example, a camera back with film or CCD. There are many different types of microscopes: Bright Field, Electron Microscopy, TEM, Confocal Microscopy, Dual Photon, but they all are common in the way that they make small invisible things visible.
Now, microscope without some sort of sensor, whether it's a retina or film or electronic CCD or CMOS, it's just an expensive illumination and focusing system. This is a nice example of an image taking with this system of an occluded vessel. And we can still see the entire vessel and we can zoom in and see the actual nuclei and individual cells. The second group is photography equipment. This is an example of cameras or scanners that can be of consumer or professional level, but scientists often use the equipment. This cross- pollination for using something built for one purpose on another is a hallmark of value creation. It is appropriate to use the best tool for the job and sometimes that tool may not have been created specifically for scientific use.
The example is this image of a microscope slide. On the direct scanning bed, I put histology slides and could acquire the image quickly and at the appropriate resolution for my work. The third family of picture producing equipment is Medical Imaging Systems. These are generally found in clinics and are used as-is, or manufacturers have modified versions and redesign them for a specific laboratory use. This is a picture of a scanner taken from the National Institutes of Health website, and you can see here an image of the heart with the ventricles and how using these pieces of equipment we can see inside a body with radiation, energy of magnetism, sound transformed into visual information.
The one common thing found with medical imaging equipment is that the images are saved in a file format called DICOM, and now with Photoshop CS3 Extended, DICOM is supported natively. The last group of equipment is designed for scientific use. Black boxes, and I use that term figuratively and literally. Literally, in that these devices, you end up placing a sample in a cavity and shut the door or lid. No external light has access and any image collected is within the device, and you don't have a direct view usually of them.
What you then see is an electronically produced image of the subject matter. That by definition is termed a black box. I also use that term figuratively in that the understanding of what exactly is going on may not be fully understood by the user. The limitations of equipment or how to truly optimize the settings. A lot of times they will put a specimen inside, set the controls as told, hit Start, and out comes the data that they hopefully want. An example of a black box system would be PerkinElmer's Cyclone. In this you put a Foster plate that has been exposed to radioactivity and it works like a drum scanner and you are able to read the plate, create an image like this showing activity, and this is made into a TIFF file that can be saved and then used.
Now that we have a handle on the sources of images and research, let's move on to general imaging workflows.
NOTE: Actual biological research images are used for this title's examples. Some of these images, including those of internal organs and dissected animals, may be considered graphic or offensive to some viewers. Viewer discretion is strongly advised.
- Understanding imaging in biomedical research
- Getting started in Photoshop
- Organizing digital assets
- Working with image stacks
- Evaluating image color and histograms
- Modifying images for research
- Compensating for acquisition problems and limitations
- Adding reference information to images
- Sharing work
- Optimizing and creating a DICOM image or animation