Research
▪
Virtuelle Pathologie Magdeburg (German)
Virtual 3D
microscopy
Common virtual slides contain a single focus plane,
providing the most optimal focus. Although a sharp image of one focus plane may
be sufficient for diagnostic pathology in many situations, focusing may be
necessary for the assessment of special structures, such as Helicobacter pylori
in gastric biopsies. To enable focusing in
virtual microscopy, it is necessary to construct three-dimensional (3D) virtual
slides providing multiple focus planes.
Here we present an example of virtual slides of a gastric biopsy using either virtual microscopy with a single focus plane, virtual 3D microscopy with 5 focus planes or virtual 3D microscopy with 9 focus planes.
published in: Kalinski T, Zwönitzer R, Sel S, Evert M, Guenther T, Hofmann H, Bernarding J, Roessner A.
Virtual 3D microscopy using multiplane whole slide images in diagnostic pathology. Am J Clin Pathol. 2008;130:259-264.
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Helicobacter gastritis
(virtual microscopy
with a single focus plane)
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Helicobacter gastritis
(virtual 3D microscopy
with 5 focus planes)
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Helicobacter gastritis
(virtual 3D microscopy
with 9 focus planes)
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Lossy compression in virtual 3D microscopy
Lossy compression is necessary to reduce the huge data amounts of virtual 3D slides. Lossy compression leads to recognizable
compression artefacts depending on the compression ratio. But where is the limit?
Here we present examples of virtual 3D slides with 9 focus planes
in JPEG2000 format compressed 20:1, 40:1, 50:1, 75:1 and 200:1.
published in: Kalinski T, Zwönitzer R, Grabellus F, Sheu SY, Sel S, Hofmann H, Bernarding J, Roessner A. Lossy compression in diagnotic virtual 3D microscopy - where is the limit?
Hum Pathol. 2009;40:998-1005.
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Helicobacter gastritis
(virtual 3D slide with a
compression of 20:1)
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Helicobacter gastritis
(virtual 3D slide with a
compression of 40:1)
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Helicobacter gastritis
(virtual 3D slide with a
compression of 50:1)
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Helicobacter gastritis
(virtual 3D slide with a
compression of 75:1)
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Helicobacter gastritis
(virtual 3D slide with a
compression of 200:1)
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Lossless
compression of JPEG2000 whole slide images
Lossy compression leads to loss of image information
and quality degradation depending on the compression level. Lossless compression
of JPEG2000 whole slide images does not impair the image quality. But is it
required in diagnostic pathology?
Here we present examples of virtual 3D slides with 9
focus planes using JPEG2000 format, lossless compressed (1:1), and lossy
compressed with compression ratios of 5:1, 10:1, and 20:1.
published in: Kalinski T, Zwönitzer R, Grabellus F, Sheu SY, Sel
S, Hofmann H, Roessner A. Lossless compression of JPEG2000 whole slide images is
not required for diagnotic virtual microscopy.
Am J Clin Pathol. 2011;136:889-895.
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Gastric biopsy
(JPEG2000 WSI, lossless compressed (1:1), size: 16.64 GB) |
Gastric biopsy
(JPEG2000 WSI,
lossy compressed
(5:1), size: 7.30 GB) |
Gastric biopsy
(JPEG2000 WSI,
lossy compressed
(10:1), size: 3.65 GB)
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Gastric biopsy
(JPEG2000 WSI,
lossy compressed
(20:1), size: 1,83 GB)
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Virtual 3D specimens
Departments of pathology possess large collections of formalin-fixed specimens for education of medical students. Virtual 3D specimens make these specimens available in the internet.
Here we present examples of virtual 3D specimens of a kidney with granular renal atrophy on the basis of glomerulonephritis and a spine showing ankylosing spondilitis (Bechterew's disease). The specimens can be rotated by using the mouse wheel in any magnification!
published in: Kalinski T, Zwönitzer R, Jonczyk-Weber T, Hofmann H, Bernarding J, Roessner A. Improvements in education in pathology: Virtual 3D specimens.
Pathol Res Pract.
2009;205:811-814.
Further specimens are presented here (German).
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Granular renal atrophy on
the basis of glomerulonephritis.
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Ankylosing spondilitis (Bechterew's disease)
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Transparencies digitally remastered
A large collection of transparencies of surgical and
post-mortem specimens was rediscovered on the attic of the department, and
digitalized in high quality (4,000 ppi) for pathology education. The images are
available in full size using JPEG2000 format, and resized to smaller dimension
in JPEG format.
All images
are included in the project 'PATHOWIKI'.
For example in the article
myocardial
infarction (German).
published in: Kalinski T, Zwönitzer R,
Roßner M, Jonczyk-Weber T, Hofmann H, Roessner A, Guenther T. Treasures from the
attic: transperencies digitally remastered and used for web-based pathology
training and education.
Histopathology. 2011. doi: 10.1111/j.1365-2559.2011.03972.x.
Speed of
virtual 2D/3D microscopy: Image Retrieve Tests
Testcalls to the JPView Render Engine. Testcalls are used for measurement of retrieval time of images.
published in:
Zwönitzer R, Hofmann H, Roessner A, Kalinski T. Virtual 3D microscopy in
pathology education. Hum Pathol. 2010;41:457-458.
Tests
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Fit to screen |
Zoom 5% |
Zoom 25% |
Zoom 100% |
Histo small 40x
31744x49152, 1 level
20:1, 0.23GB
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Histo medium 40x
91392x114688, 1 level
20:1, 1.5GB
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Histo large 40x
115712x143360, 1 level
20:1, 2.4GB
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Biopsy 40x
26368x24576, 9 level
20:1, 0.86GB
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Cytology 60x
44032x49152, 9 level
20:1, 2.9GB
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