#How to reference imagej software in a paper full#
However, this technique involves the manipulation of huge images (of the order of 10 billions of pixels for a full-size slide at magnification 40x with a single focus level) for which the approach taken by most standard software, loading and decompressing the full image into RAM, is impossible (a single slice of a full-size slide needs of the order of 30 GiB of RAM). Almost all cell nuclei are detected and the shapes of the contours are much more precise. The white contours show the result of the same automatic detection. ( c): the same portion of the slide scanned at magnification 40x. A significant fraction of the cell nuclei is missed and the contours are rather pixelated. The white contours show the result of an automatic detection of the dark cell nuclei with the ImageJ software. ( b): a portion of the slide scanned at magnification level 10x. ( b,c): Influence of the magnification on the quality of results. ( a): macroscopic view of the whole slide (the black rectangle on the left is 1x2 cm). An accurate, non-pixelated determination of the perimeters of the cell nuclei is needed for morphometry and statistics.Ī sample slide. For instance, the state of the chromatin inside the nucleus and the cell morphology, better seen at high magnification, are essential to help the clinician distinguish tumorous and non-tumorous cells. The benefit of the high magnification for both diagnosis and automated image analysis is clear. Figure1 1 shows two portions of a slide at different magnifications, 10x and 40x. They allow much better visualization and analysis than lower magnification images.
, for instance at the so-called “40x” magnification. Modern slide scanners produce high magnification microscopy images of excellent quality This growing use of virtual microscopy is accompanied by the development of integrated image analysis systems offering both virtual slide scanning and automatic image analysis, which makes integration into the daily practice of pathologists easier. will include more and more digitized tissue images. A growing number of works report the pertinence of such images for diagnosis and classification of diseases, e.g. Quantitative histology is a promising new field, involving computer-based morphometry or statistical analysis of tissues
mathematicians and clinicians who do not work at the same location. They have also a great potential for research, especially in the context of multidisciplinary projects involving e.g. In more and more hospitals, virtual slides are even attached to the patient’s file Virtual microscopy has become routinely used over the last few years for the transmission of pathology images (the so-called virtual slides), for both telepathology and teaching
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