Documentation of microscopic objects and observations often lead, over the years, to a huge amount of photomicrographs. To become a treasure for data mining, the annotation of these images should be done carefully. To support microscopist's needs in that matter, we decided to design and implement software which integrates data mining, annotation, measuring and even 3D display techniques. This first software-version of our Expert System for Light Microscopy (E.L.M.I.) is now available.
Database and Annotation System
Due to data mining purposes, the images alone are of little worth. Additional information, like optics and methods used at the moment the picture was taken, a more detailed description of the object is desirable. The circumstances under which the objects of interest were observed, the conditions and the process when they happened, are just as important as the picture itself. These notes should be saved carefully together with the image, because often this information is clear and present the moment of observation, but fades after even a short time. For a detailed description of the
object observed, the software offers several text processor windows providing enough capacity for this purpose. These are sensitive for the implemented database queries and even offer a graphical interface for further illustration, too.
The program carefully stores all the relevant optical information with the image. Therefore, measurements of distances, areas and volumes of objects within those images will always be possible for future questions and investigations. To record the optics independent of any manufacturer, the physical parameters of the optics used are kept in its own physical database system and may be chosen manually with the picture shot. The program calculates suitable micrometer factor, using its integrated image analysis calculated from photos taken using a micrometer slide of all optical combinations. Each micrometer mark has a certain "roughness" and the distances between micrometer marks differ slightly depending on fabrication tolerances. The E.L.M.I.'s Image Analysis uses stochastic theory to calculate the most precise micrometer factor and the error of it.
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Therefore, each measurement (done with the mouse in real time) shows the result and its standard error due to the underlying object micrometer precision. If you don't like the standard error printed, you may switch it off.
As the database system knows exactly the physics behind that photo, the suitable micrometer factor calculated will always be used for measuring when the corresponding optics composition are chosen. The program offers the measurement of length, angle, area and volume (depending on several underlying, modifiable, volume models). Additionally, you may annotate your image with text markers, graphical markers, other graphical elements and text. All these annotations may be stored in different "layers", which can be combined, or presented, independently from each other. The original image data is never modified or changed by the program. This annotation data is stored separately. For publication purposes, there is a modifiable measuring rod available. Of course, all graphical elements of "substance" (like irregular areas) appear transparently, if wanted. To investigate your images, the program supports flicker free moving, rotating and zooming, both with normal mouse and 3D mouse. With a 3D mouse, all movements, zooming and rotations, may be done simultaneously and make the image investigation "feel" like using a microscope slide-stage with zoom lens.
Another important feature for data retrieval for your own publications, are references describing or explaining objects similar to the one being observed and displayed on the photograph. It is possible to link these references as files to the image to get further information instantly available with a simple mouse click, whenever needed. Sometimes, additional measurements (like spectra) are of importance. This data is often stored in unusual formats readable only with the manufacturer's software. The program remembers data files and applications needed for its investigation.
In histology, photographs of a certain topic are often taken from one, or more, microscope slides commonly stored within a dissection collection. In our laboratory, we produce QR-tags which code usually for at least 500 - 550 letters, each. That capacity offers enough specific information for a small report on each microscope-slide. You may link such a QR-tagged slide to the related images within the program's database. Scanning the QR-code of a microscope-slide, causes E.L.M.I. to report all images and information collected for this particular slide instantly. The other way round, a given photograph is easily identified to the corresponding safe-keeping position of the microscope-slide within the dissection collection containing the object the image
was taken from.
Generating and printing QR-tags needed for labeling microscope slides is easy with the software. Directly scanning QR-tags is supported using an industrial laser-scanner, also. Just to keep searching and verifying easy, it is possible to read the QR-Information generated with the program, using a standard smart phone, e.g. at the cabinet where the slides are stored in the lab. There is no problem in enciphering the QR-information with the software, so that more sensible data may not be deciphered using a smart phone for scanning.
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