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* Home
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* TissueFAXS Histo
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* StrataQuest
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Full 1
Explore the Tissue Landscape
Whole-slide imaging and analysis solutions tailored to your research
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WELCOME
TissueGnostics provides fully integrated cutting-edge tissue cytometers for (i)
whole-slide imaging (brightfield, fluorescence, confocal, multispectral) and
(ii) high-end analysis of tissue sections, cultured cells, TMAs, smears etc.
Explore TGs solutions for spatial phenotyping, single cell analysis, molecular
single cell profiling, machine-learning based tissue classification and many
more.
IHC IMMUNE STATUS IN SITU
APP SHOWCASE
IF Cellular Microenvironment
The IF Cellular Microenvironment App allows to determine the cellular phenotype
of specific IF-stained cell populations.
Webinar
TG ACADEMY WEBINAR
Practical Approaches for Using Tissue Cytometry for Research Applications
Dr. Henning Ulrich
University of Sao Paulo
Watch Webinar
news
NEWS
NEW Boxed Cytometer
Our newest prodct Colubris, an All-in-one, platform for the acquisition,
management, visualisation and analysis of imaging data is lauching soon!
Blog post
BLOG UPDATE
Immunofluorescence Image Analysis
In research, techniques like immuno-fluorescence staining combined with tissue
cytometry are crucial for studying biology.
Blog Update FISH
WHITE PAPER
Cytolytic CD8+ T Cells Role in Suppressing HIV Replication
A recent study revealed important information on how cytolytic CD8+ T cells are
central in determining long-term viral control.
Slider_4_Link to Site
Explore our online database of reference publications
Explore our online database of reference publications to find out how tissue
cytometry can elevate your research
Explore Now
News
ARTICLE
World's Visionary Healthcare Entrepreneurs 2023
Dr. Rupert Ecker, CEO of TissueGnostics, has achieved a remarkable milestone by
gracing the cover of the World's Leader Magazine.
AMI
NEWS
TissueGnostics and REDI Australia Partnership
REDI Fellow Jyotsna Batra successfully completes her fellowship with
TissueGnostics to battle prostate cancer.
Testimonial Jan Soetart
Dr. Franco Fortunato
TissueFAXS enables state-of-the-art multiplex analysis of protein expression and
tissue localization, making it my preferred tool for cancer research for over a
decade.
SQ Appcenter Post
TOOLS
StrataQuest Appcenter
Explore our analysis solutions in our Strataquest Appcenter and get inspired by
the variety of applications.
* TISSUE CYTOMETERS
Read More
* ANALYSIS SOLUTIONS
Read More
* APP CENTER
Read More
* 1
EXPLORE OUR SOLUTIONS »
PORTFOLIO
TissueGnostics (TG) provides streamlined solutions for both biomedical imaging
and image analysis. The goal of TG is to bring the same type of phenotypical
analysis of single cells from Flow Cytometry into tissue context. The merging of
image analysis software and high-quality optics and robotics has allowed TG to
create the TissueFAXS system - a fully automated system which can scan
slides/well plates and automatically quantify marker expression per cell. Going
a step beyond that is StrataQuest - a software development platform for creating
complex image analysis algorithms that can automatically detect multicellular
structures within scanned tissue sections for a highly detailed contextual
tissue analysis.
The imaging systems are modular and upgradable. Every system can be customized
to offer the following capabilities: brightfield scanning, widefield
fluorescence, confocal, and multispectral. Every system can come either in an
upright configuration for scanning slides only, or inverted for scanning well
plates and slides. Each TissueFAXS system comes with either an 8-slide stage, or
a high-throughput automatic 120 slide loading system only available for the
upright TissueFAXS system configuration. TissueFAXS systems can come with high
powered LED light engines combined with multi bandpass filter cubes for high
speed fluorescence scanning.
Image analysis software comes in 3 forms: TissueQuest for fluorescence image
analysis, HistoQuest for brightfield image analysis, and StrataQuest for
multicellular contextual tissue analysis for both brightfield and fluorescence
images. TissueQuest and HistoQuest are streamlined for rapidly acquiring nuclear
segmentation and marker quantification per cell. StrataQuest offers much more in
terms of image analysis and is therefore more complex, which is why
TissueGnostics offers the development of customized algorithms as a service to
researchers. Every StrataQuest solution (or APP) includes a simplified user
interface that is made by the underlying algorithm, and contains macros so that
even researchers with little or no experience in image analysis can obtain high
quality data from analysing their scanned images.
TG provides image analysis solutions for a multitude of research questions. The
image analysis software StrataQuest, HistoQuest and TissueQuest (for brightfield
and fluorenscence projects) can be applied e.g. to explore the tumor
microenvironment and/or the spatial organization of cellular subpopulations, to
detect and quantify fluorescence in situ hybridization (FISH), to assess
different bone structures, or to analyze multiplex IF stainings. Please find
additional applications in the sections: App center and user examples
in StrataQuest APP analysis examples.
* TG AUSTRIA
Global Headquarter
Taborstrasse 10/2/8
A-1020 Vienna
AUSTRIA, EU
Tel.: +43/1/216 11 90
office@tissuegnostics.com
TG ROMANIA
Str. Sf. Andrei, nr.15A
700028 Iasi
ROMANIA, EU
Tel.: +40/332/40 58 66
office@tissuegnostics.com
Read More
* TG USA
12522 Moorpark Street
Suite #106
Los Angeles, CA 91604
USA
Tel.: +1/818/856/8056
office@tissuegnosticsusa.com
TG USA East
ScientiaLux d.b.a.
4 Farnum Terrace
Worcester, MA 01602
USA
Tel.: +1/508/471/7732
office@tissuegnostics.com
Read More
* TG ASIA PACIFIC
China Division
Room 506,
No.6 Auto Museum East Rd,
Fengtai District Beijing
CHINA
Tel.: +86/400/898 1980
office@tissuegnostics.cn
Western Pacific Division
Taipei
Tel.: +886/928/899 397
office@tissuegnostics.cn
Australia Division
Brisbane, Queensland
Tel.: +61/416 037 618
office@tissuegnostics.com
Read More
* TG AFRICA
Measuring Instruments Technology (MIT)
CSIR Campus, Building 33
Meiring Naude Rd
Brummeria, Pretoria 0181
SOUTH AFRICA
Tel.: +27 12 349 5191
Cell: +27 82 784 2011
office@tissuegnostics.com
Read More
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WANT TO KNOW MORE? CONTACT US
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WANT TO KNOW MORE?
CONTACT US »
Blog update spatial
BLOG UPDATE
An Introduction to Spatial Tissue Cytometry
Cytometry encompasses several methods for investigating cells, such as their
count, cell cycle state, phenotype, morphology, size ...
NEWS
NEW Boxed Cytometer - Colubris
We have a lot of exciting plans to share for our big birthday, but we also have
many important milestones to reflect on and remember...
Festival Hacks
Subscribe to our scientific Infoletter
Subscribe to Newsletter
App Showcase
APP SHOWCASE
IHC IMMUNE SATUS IN SITU
The IHC Immune Status in Situ App uses the AI classifier to segment tissue into
morphological entities such as tumor, stroma, and lymphocyte clusters. It
further identifies single cells ...
Publications
TOOLS
Reference Publications
Explore our online database of reference publications to find tout how tissue
cytometry can elevate your research
Appcenter
TOOLS
StrataQuest Appcenter
Explore our vast catalog of analysis solutions in our Strataquest Appcenter and
get inspired by the variety of applications.
Nadine Bayer
TG ACADEMY WEBINAR
The Effect of Stem Cell Transplantation on Skin Microorganisms
Watch Webinar
Nadine Bayer, PhD
Medical University
of Vienna
Eurolab Article
ARTICLE
Spatial Tissue Cytometry: Success Stories - Eurolab Article
Read about tissue cytometry's potential in understanding the complexities of
cell populations in the tissue environment
CONTACT
TissueGnostics GmbH
Taborstraße 10/2/8
1020 Vienna, Austria
+43 1 216 11 90
office@tissuegnostics.com
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* Home
* Products
* COMING SOON Boxed Cytometer
* Colubris
* Confocal Cytometer
* TissueFAXS Q Platform
* Multispectral Cytometer
* TissueFAXS SPECTRA Platform
* TissueFAXS CHROMA
* High-Throughput Cytometer
* TissueFAXS SL
* Fluorescence & Brightfield Cytometer
* TissueFAXS PLUS
* TissueFAXS i PLUS
* Fluorescence Cytometer
* TissueFAXS Fluo
* TissueFAXS i Fluo
* Brightfield Cytometer
* TissueFAXS Histo
* TissueFAXS i Histo
* StrataFAXS II
* Scanning and Viewing Software
* TissueFAXS Imaging Software
* TissueFAXS Viewer
* Contextual Image Analysis
* StrataQuest
* StrataQuest App Center
* AI solutions in StrataQuest
* Single Cell Analysis
* TissueQuest
* HistoQuest
* -
* RESEARCH
* Publications
* White Papers
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IF SKELETAL MUSCLE
The IF Skeletal Muscle App allows the segmentation of skeletal muscle tissue
sections into muscle fibers and connective tissue based on specific IF staining.
Outcome parameters are provided, such as the number of muscle fibers and area of
the total tissue, muscle fibers, and connective tissue.
Image: Courtesy of Stefania Petrini, Bambino Gesù Children’s Hospital, Rome
App Category 2
×
×
IHC ADIPOCYTE
The IHC Adipocyte App quantifies adipocytes and their lumen in adequate HE
samples. The App automatically mends small rips in adipocyte membranes and
eliminates cell membrane artifacts in adipocyte lumina and lumina on sample
borders. The App also outputs area measurements for all detected adipocyte
lumina.
App Category 1
Example for IHC Adipocyte App
×
×
IF 2
The IF 2 App provides single cell-based co-expression analysis for two IF
markers. It segments cells into their nucleus, perinuclear area, and/or
cytoplasm. Each segmented cell compartment is measured for up to 20 intensity,
statistic, and morphometric parameters that can be displayed in and exported
into scattergrams and histograms.
App Category 1
×
×
IF 3
The IF 3 App provides single cell-based co-expression analysis for three IF
markers. It segments cells into their nucleus, perinuclear area, and/or
cytoplasm. Each segmented cell compartment is measured for up to 20 intensity,
statistic, and morphometric parameters that can be displayed in and exported
into scattergrams and histograms.
App Category 1
×
×
IF 4
The IF 4 App provides single cell-based co-expression analysis for four IF
markers. It segments cells into their nucleus, perinuclear area, and/or
cytoplasm. Each segmented cell compartment is measured for up to 20 intensity,
statistic, and morphometric parameters that can be displayed in and exported
into scattergrams and histograms.
App Category 2
×
×
IF GLOMERULI
The IF Glomeruli App provides the detection of tissue, cells, and glomeruli
stained by a specific marker. It segments the cells into their nucleus and/or
cytoplasm and determines the cellular phenotype of specific IF-stained cell
populations. The detected cells can be classified as being either inside or
outside the glomeruli within certain distances (distance ranges are definable).
For each cell, the spatial information and up to 20 intensity, statistics, and
morphometric parameters are measured. The data can be displayed in diagrams and
exported.
App Category 3
×
×
IF HI-PLEX 50
The IF Hi-Plex 50 App combines and analyses images of the same IF-stained tissue
section, acquired up to 50 times with different markers. The App enables the
detection of the cellular phenotypes of specific IF-stained cell populations. It
segments cells into their nucleus, perinuclear area, and/or cytoplasm. Each
segmented cell compartment is measured for up to 20 intensity, statistic, and
morphometric parameters that can be displayed in and exported into scattergrams
and histograms.
App Category 3
×
×
IF DOTS
The IF Dots App provides dot detection per cell within the cell compartments for
up to four markers in a sample (e.g., FISH, RNA, oil droplets). Each segmented
cell compartment is measured for up to 20 intensity, statistic, and morphometric
parameters. Dot measurement parameters are provided per cell compartment (e.g.,
nucleus, cytoplasm) and per dot and include count, mean intensity, total dot
area, the sum of intensity.
App Category 2
Example for IF Dots App
×
×
IF Immune Status in situ
The IF Immune Status in Situ App provides a phenotypic characterization of
immune cells in reference to detected metastructures (e.g., tumors, glands) and
measures the distance of detected cellular objects to the metastructure boundary
(within and/or outside). Distance ranges are also definable. Each segmented cell
compartment is measured for up to 20 intensity, statistic, and morphometric
parameters, as well as the distance of each cell to the areas boundary.
App Category 3
×
×
IF SKIN MORPHOLOGY
The IF Skin Morphology App provides tissue detection, including the segmentation
of epidermis and dermis, based on specific IF staining. It segments cells into
their nucleus, perinuclear area, and/or cytoplasm and determines the cellular
phenotype of specific IF-stained cell populations. The detected cells can be
classified and visualized as being within or outside detected structures
(epidermis and dermis). Each segmented cell compartment is measured for up to 20
intensity, statistic, and morphometric parameters that can then be displayed in
diagrams and exported.
App Category 3
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IF GRANULOMA
The IF Granuloma App detects granulomas based on nuclear structure analysis and
an adequate IF staining (e.g., CD11c, CD68). The App measures the number and
area of Granulomas and their density. Each segmented cell compartment is
measured for up to 20 intensity, statistic, and morphometric parameters.
App Category 2
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IF CYTOSKELETON
The IF Cytoskeleton App detects cytoskeletal structures based on a specific
stain. The cell cytoplasm can be detected using other stains. Data can also be
exported, including the number of cytoskeletal filaments inside and outside the
cell and on the cell membrane, filament length, and total filament area.
App Category 3
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IF GLIAL CELLS
The IF Glial Cells App allows the detection of astrocytes and microglia based on
specific IF staining. The measurements assessed by the App include the number of
astrocytes and microglia and the number of branches of each cell (short and long
attached).
App Category 3
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IHC 2
The IHC 2 App unmixes two markers (e.g., chromogen and counterstain) in an IHC
or HC digital slide and segments single cells into their nucleus, perinuclear
area, and/or cytoplasm. Each segmented cell compartment is measured for up to 20
intensity, statistic, and morphometric parameters that can be displayed in and
exported into scattergrams and histograms.
App Category 1
Example for IHC 2 App
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IHC 3
The IHC 3 App unmixes three markers (e.g., two chromogens and a counterstain) in
an IHC or HC digital slide and segments single cells into their nucleus,
perinuclear area, and/or cytoplasm. Each segmented cell compartment is measured
for up to 20 intensity, statistic, and morphometric parameters that can be
displayed in and exported into scattergrams and histograms.
App Category 2
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IHC MACROPHAGES
The IHC Macrophages App detects macrophages based on adequately stained IHC
samples. The App can be combined with area detection and distance range
algorithms to determine the distance of Langerhans cells from the border of the
epidermis inside and outside the epidermis (see above example). Each segmented
cell compartment is measured for up to 20 parameters, as is the distance of each
cell to the boundary.
App Category 3
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IHC TUMOR-STROMA
The IHC Tumor-Stroma App combines the segmentation of tumor and stroma (based on
the morphology) and the detection of specifically stained cell populations. It
segments the cells into their nucleus, perinuclear area, and/or cytoplasm. Each
segmented cell compartment in tumor and/or stroma is measured for up to 20
intensity, statistic, and morphometric parameters that can be displayed in and
exported into scattergrams and histograms.
App Category 2
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PULMO
The Pulmo App segments nuclei and the metastructure components of the lung,
including tissue, bronchioles, blood vessels, and alveoles. Each segmented
metastructure is measured for up to 20 morphometric parameters.
App Category 3
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IHC ANGIO
The IHC Angio App detects blood vessels based on appropriate stains (e.g., CD31)
and measures overall vessel and lumen areas. The vessel detection can be set to
close open stained vessel walls and connect separated vessel sections within a
definable distance. As well as vessel number, density, and areas, the App also
outputs endothelium and lumina areas.
App Category 2
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IHC META CELLS
The IHC Meta Cells App combines the detection of IHC/HC stained metastructures
(e.g., Langerhans islets, Tumor - Stroma) with single-cell detection
(segmentation of cells into nucleus, perinuclear area, and/or cytoplasm).
Detected cells can be classified and visualized as being within or outside
detected metastructures. Each detected area and cell compartment is measured for
up to 20 intensity, statistic, and morphometric parameters.
App Category 2
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RNA SCOPE
The RNA Scope App enables the detection of nuclei based on appropriate staining
and dot detection per cell within nucleus and/or cytoplasm for one dot marker in
CISH and SISH experiments . Each segmented cell compartment is measured for up
to 20 intensity, statistic, and morphometric parameters. Dot parameters are
provided per cell and per dot and include count, mean intensity, total dot area
and the sum of intensity.
App Category 2
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TUMOR FOCI
The Tumor Foci App allows for the detection of the whole tissue and, more
importantly, tumor foci based on nuclear structure analysis, mainly on HE
staining. The number, area, and density of tumor foci are measured.
App Category 1
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IHC MEMBRANE
The IHC Membrane App unmixes up to three markers in an IHC or HC digital slide
and segments cells into nucleus, perinuclear area, and/or cytoplasm, as well as
into membrane (e.g., HER2/neu). Each segmented cell compartment is measured for
up to 20 intensity, statistic, and morphometric parameters. Three more
parameters are measured for membrane intensity and angle of staining. All
parameters are displayed in scattergrams and histograms and can be exported.
App Category 2
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BONE GOLDNER
The Bone Tissue Analysis Goldner App allows for the detection of mineralized
bone tissue and osteoid based on Goldner-stained bone tissue sections. The App
assesses parameters such as BV (bone volume), TV (trabecular bone volume), OV
(osteoid volume), OV/BV, OV/TV, OS (osteoid surface), BS (bone surface length),
and the mean of osteoid width and thickness.
App Category 2
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BONE MINERALIZATION
The Bone Mineralization APP separates Safranin O-stained bone tissue into its
morphological substructures (cartilage, mineralized cartilage, bone marrow, and
mineralized bone). Measurements assessed with this App include TV (trabecular
bone volume), BV (total bone volume), MCV (mineralized cartilage), CV (cartilage
volume), and bone marrow (BM).
App Category 3
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BONE VON KOSSA
The Bone Tissue Analysis Von Kossa App allows for the detection of mineralized
bone tissue based on Von Kossa stained bone tissue sections. The App provides
parameters such as TV (trabecular bone volume), BV (bone volume), BS (bone
surface), BV/TV, BS/BV, Tb.N (trabecular number), tb.Th (trabecular thickness),
and Tb.Sp (trabecular separation).
App Category 2
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IF LEISHMANIASIS
The IF Leishmaniasis App detects intracellular Leishmania parasites and segments
them in the detected host cells. The number of parasites per cell is determined,
and living and dead parasites can be distinguished (live/dead assays). The App
outputs 20 intensity, statistic, and morphometric parameters for each segmented
cell compartment per marker, as well as the number, mean intensity, sum of
intensity, and size of parasites.
App Category 2
Example for IF Leishmaniasis App
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IF CELLULAR MICROENVIRONMENT
The IF Cellular Microenvironment App allows to determine the cellular phenotype
of specific IF-stained cell populations and establishes their spatial
relationship between each other and their neighboring cells/cell populations,
including those with metastructures (e.g., blood vessels, tumors) in their
vicinity. It is especially suited for proximity and infiltration analyses.
App Category 4
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IF NEURITE
The IF Neurite App identifies neuronal cells and cell clusters and their
neurites/dendrites. It quantifies the number of neurites/dendrites branching out
from a specific neuron, identifies branch points, and exports total
neurite/dendrite area, total neurite/dendrite length, average neurite/dendrite
thickness, the number of branch points, and the number of endpoints.
App Category 3
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IF PYKNOTIC NUCLEI
The IF Pyknotic Nuclei App provides tissue detection and cell segmentation in
combination with the detection of pyknotic nuclei (defined as completely
condensed, round, high-intensity nuclei) based on nuclei staining. Additionally,
the App allows for the determination of the cellular phenotype of specific
IF-stained cell populations and dot detection. It segments the detected cells
into nucleus, perinuclear area, and/or cytoplasm. The App provides parameters
such as the number, mean intensity, and percentage of specific cell populations
(including cells containing pyknotic nuclei). It also outputs dot parameters per
segmented cell and/or dot, including count, mean intensity, total dot area, and
sum of intensity.
App Category 3
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IF TUMOR VASCULARIZATION
The IF Tumor Vascularization App provides tissue detection, including the
separation of tumor tissue and tumor stroma (healthy tissue). Additionally, it
detects blood vessels based on appropriate stains (e.g., CD31) and measures the
number, area, and density of these blood vessels. The vessel detection also can
be set to close open stained vessel walls and to connect separated vessel
sections within a definable distance.
App Category 3
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IHC TUMOR MACROPHAGES
The IHC Tumor-Macrophages App provides tissue detection, including the
separation of tumor and healthy tissue. It detects macrophages based on specific
staining (e.g., CD68) and outputs the area of macrophages within tumor and
healthy tissue.
Image: Courtesy of Dr. Patrick Michl, Dr. Maren Egidi, and Dr. Heidi Griesmann,
Universitätsklinikum Halle (Saale).
App Category 3
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IHC TUMOR VASCULARIZATION
The IHC Tumor Vascularization App provides tissue detection, including the
separation of tumor tissue and tumor stroma (healthy tissue). Additionally, it
detects blood vessels based on appropriate stains (e.g., CD31) and measures the
number and area of these blood vessels. The vessel detection can also be
programmed to close open stained vessel walls and to connect separated vessel
sections within a definable distance. The App outputs the number, density, and
areas of vessels within both tumor and healthy tissue.
Image: Courtesy of Dr. Patrick Michl, Dr. Maren Egidi, and Dr. Heidi Griesmann,
Universitätsklinikum Halle (Saale).
App Category 3
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IHC ANGIO TRICHOME
The IHC Angio Trichome App detects blood vessels based on trichome staining and
measures the overall vessel and lumen area. Furthermore, it detects specifically
IHC-stained single cell populations and establishes their spatial relationship
to the detected blood vessels. The App outputs number and vessel density, vessel
wall thickness and areas of vessels, endothelium and lumina, the number of IHC
stained cells, proximity measurement, etc.
App Category 3
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RNA SCOPE+
The RNA Scope+ App provides detection of nuclei based on appropriate staining
and dot detection per cell within the nucleus and/or cytoplasm for two dot
markers in CISH and SISH experiments. Each segmented cell compartment is
measured for up to 20 intensity, statistic, and morphometric parameters. It also
outputs dot parameters per segmented cell and/or dot, including count, mean
intensity, total dot area, and sum of intensity.
App Category 2
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IHC ANGIO ELASTIN
The IHC Angio Elastin App detects blood vessels in Verhoeffs van Geison-stained
samples, elastin, and collagen. The outputs include the number and area of
vessels, elastin, and collagen within a definable distance to the vessel.
App Category 2
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IF CARDIO CELL CULTURE
The IF Cardio Cell Culture App provides cell segmentation, detection of
cardiomyocytes (based on appropriate staining, e.g., Troponin Red), fibroblasts
within cultured cardio cells, plus one additional marker. The App outputs
parameters such as the number of cardiomyocytes, fibroblasts, and
marker-positive cardiomyocytes and fibroblasts.
Image: Courtesy of Agatha Ribeiro da Silva, Prof. Jose E. Krieger (Heart
Institute, University Sao Paulo)
App Category 3
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IF CARDIO CELL CULTURE DOTS
The IF Cardio Cell Culture Dot App provides cell segmentation and detection of
cardiomyocytes (based on an appropriate stain, e.g., Troponin Red) and
fibroblasts within cultured cardio cells, plus one dot marker (CISH, FISH). The
App outputs parameters such as the number of cardiomyocytes and fibroblasts. It
also outputs the number of dot-positive cardiomyocytes and fibroblasts and the
number, area (μm²), and mean intensity of dots per cell.
Image: Courtesy of Agatha Ribeiro da Silva, Prof. Jose E. Krieger (Heart
Institute, University Sao Paulo).
App Category 3
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IF DENDRITES AND AXONS
The IF Dendrites & Axons App identifies neuronal cells, their dendrites and
axon, based on appropriate markers. It quantifies the number of dendrites
branching out from a specific neuron. The App provides the total number of
dendrites per neuron, including the length of these dendrites and their axons.
Image: Courtesy of Thomas Bastian, Ph.D., University of Minnesota.
App Category 3
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IHC SMALL INTESTINE - DOTS
The IHC Small Intestine - Dots App provides nuclei segmentation and detection of
tissue and villi based on nuclei staining (crypts need to be defined manually).
Furthermore, it allows dot detection for one dot markers (CISH, RNAScope, SISH)
within villi and crypt areas. Dot parameters are provided for villi and crypts
and for dots and include count, mean intensity, total dot area, the sum of
intensity.
App Category 2
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LIPID DROPLETS
The Lipid Droplets App quantifies lipid droplets within H&E stained tissues
(e.g., liver). The App automatically mends small rips in liver droplet membranes
and eliminates cell membrane artifacts, including lumina on sample borders. The
App also outputs area and number measurements for all detected lipid droplets.
App Category 1
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ANGIO SIRIUS RED
The Angio Sirius Red App detects collagen and blood vessels based on Sirius Red
staining. The app outputs the area of Sirius Red stained collagen and the number
of detected vessels.
App Category 2
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IHC ANGIO DIAMETER
The IHC Angio Diameter App detects blood vessels based on appropriate stains
(e.g., CD31). The App outputs vessel area, number, density, and blood vessel
diameter.
App Category 2
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IF CULTURED CELLS & SUBSTRUCTURES
The IF Cultured Cells & Substructures App detects cells based on nuclei
staining, as well as one dot marker (FISH, CISH experiments) and cytoskeletal
structures based on a specific stain. It outputs the number of detected cells,
the number and intensity of dots per cell, and the density of cytoskeletal
filaments.
App Category 3
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IF MEMBRANE
The IF Membrane App detects nuclei and segments the cells into different
cellular compartments, including membrane, nuclei, and cytoplasm. It also
detects one additional marker (e.g., HER2/neu). Each segmented cell compartment
is measured for different parameters, such as staining intensity, stained area,
and the number/percentage of marker-positive cells within the detected cellular
compartments. Three more parameters are measured for the membrane, including
membrane area, membrane length, and the angle of staining.
App Category 2
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IF SPHEROIDS
The IF Spheroids App allows a comprehensive analysis of spheroids (as well as
organoids and embryoid bodies). It automatically identifies the spheroids and
cells based on the nuclei staining and analyzes two additional IF markers. It
segments the cells into different cellular compartments, including membrane,
nuclei, and cytosol, and further measures the marker expression for each
compartment. It can also measure dot markers (if available). It establishes
proximity distances for the cells detected within the spheroids, bringing the
IF-stained cell populations into spatial context.
App Category 3
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IHC IMMUNE STATUS IN SITU
The IHC Immune Status in Situ App uses the AI classifier to segment tissue into
morphological entities such as tumor, stroma, and lymphocyte clusters. It
further identifies single cells based on nuclei staining (hematoxylin), detects
immune cells based on appropriated stains (CD45, CD3, CD20, etc.), and measures
the distance of detected cells to the metastructure boundary. The App can also
define distance ranges through outputting parameters, including the area of the
detected morphological entities and the number/percentage of lymphocytes
detected within the tissue entities, as well as in certain proximities.
App Category 3
Read more
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WILMS TUMOR
The Wilms Tumor App is based on the AI Classifier and allows for the
segmentation of H&E stained Wilms tumor tissues into tumor, stroma, and blood
vessels. It outputs the area (µm2) of the segmented tissue entities.
App Category 1
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IHC NECROTIC TUMOR
The IHC Necrotic Tumor App segments tumor tissues into tumor, necrotic tissue,
and stroma using the AI Classifier. Furthermore, it identifies single cells as
well as one additional cellular marker (e.g., neutrophils). It outputs the area
of tumor, necrotic tissue, and stroma and measures the number and percentage of
neutrophils within the morphological entities.
App Category 3
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IHC NECROTIC TUMOR ANGIO
The IHC Necrotic Tumor Angio App can segment tumor tissues into tumor, necrotic
tissue, and blood vessels using the AI Classifier. It outputs the area of tumor,
necrotic tissue, and blood vessels, as well as the number and percentage of
blood vessels in total and within the two morphological entities.
App Category 3
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IF RODS AND CONES IN RETINA
The IF Rods & Cones in Retina App detects the rods and cones based on specific
staining. It outputs the number, density, and length of detected structures, as
well as the number, percentage, and density of marker-stained rods and cones.
App Category 2
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IF TUMOR FOCI ANGIO
The IF Tumor Foci Angio App identifies single cells and segments tissues into
tumor foci and blood vessels based on appropriate markers. It applies proximity
maps to identify nuclei close to blood vessels. It measures the number of nuclei
located within a certain distance relative to blood vessels, the number of
nuclei in the different morphological entities, and the area of these
morphological entities.
App Category 3
Read more
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IF RETINAL VASCULATURE
The IF Retinal Vasculature App detects blood vessels in retinal tissue based on
appropriate stains (e.g., CD31). The App outputs vessel area, density, and
length.
App Category 2
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ENDOMETRIUM HE
The Endometrium HE App allows for the segmentation of hematoxylin and
eosin-stained endometrium tissues into their morphological entities (glands,
stroma, and blood vessels). The measurements provided by the App include the
area of glands, stroma, and blood vessels.
App Category 2
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IHC EXTRACELLULAR FILAMENTS
The IHC Extracellular Filament App detects nuclei and extracellular filaments
stained with specific markers. It outputs the number of nuclei, total filaments
area, and the length of these filaments.
App Category 2
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IF CELLULAR CONTACT
The IF Cellular Contact App allows for the determination of the cellular
phenotype of specific IF-stained cell populations and establishes the cellular
contacts to their neighboring cells (the number of markers is technically
unlimited). If needed, the App provides a separation of nuclei in tissues with
high cellular densities. The App outputs parameters such as staining intensity
per marker and morphometric parameters for each segmented cell/cell compartment,
as well as the number and percentage of cells of different phenotypes in direct
contact.
Images: courtesy of Naoki Kaneko/Shiv Pillai (PI), Ragon Institute of MGH, MIT
and Harvard, Boston, MA USA.
App Category 3
The App was used in a CELL publication, read more
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EBER-ISH
The EBER-ISH App analyzes tissue samples stained by EBER-ISH probes (EBV-encoded
RNA in-situ hybridization). These probes visualize the Epstein-Barr virus (EBV)
EBER RNA. First, the App identifies nuclei, then detects EBER-ISH positive
nuclei. The measurements provided by the App include the number of detected
cells and the number, density, and percentage of EBER-ISH positive cells.
App Category 1
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IF CELL CULTURE - OSTEOCLAST
The IF Cell Culture - Osteoclast App allows for the segmentation of nuclei, the
identification of cultured multinucleated osteoclasts (stained by a specific
marker), and the quantification of one or two additional markers. Outputs
include the number of detected cells, osteoclasts, and nuclei per osteoclast,
the area of osteoclasts, and the intensity of markers within the osteoclasts.
App Category 2
read more about Automated Detection and Characterization of Osteoclasts in
Microscopic Images
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ORGANIOD
The Organoid App detects cultured organoids using the machine learning
classifier. It outputs number and total area (µm2) of organoids and categorizes
them into different size classes.
App Category 3
read more
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IF BRAIN
The IF Brain App allows the classification (using the AI based classifier) of
brain regions and detection of various cellular phenotypes, e.g. astrocytes,
based on stained linage markers. The App outputs area (µm2) of detected tissues
classes, count of total cells as well as in each detected area. Count and % of
specific phenotype detected in total as well as in tissue classes.
App Category 3
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IF EMBRYOID BODIES
The Embryoid Bodies App automatically detects embryoid bodies/organoids based on
IF staining. It identifies nuclei based on DAPI staining or other nuclei dye and
identifies additional phenotype markers in the nuclei/cell and/or membrane of
the detected cells. It outputs number and area (µm2) of detected embryoid
bodies/organoids, count of nuclei and count/% of cellular phenotypes.
App Category 2
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IF INSULIN ISLETS
The IF Insulin Islet App allows for detection marker stained insulin islets, the
whole tissue, and cellular phenotypes stained by specific markers within the
insulin islets. The App outputs, whole tissue area (µm2), number and area (µm2)
of detected insulin islets. Number of cells and marker-specific phenotypes in
the whole tissue as well as within the insulin islets. Image provided by Emma
Hamilton-Williams.
App Category 3
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MUCIN SWISS ROLL
The Mucin Swiss Roll App allows for detection of the swiss roll, and the
segmentation into different subclasses (mucosa, immune cell follicles,
connective tissue, background). Further it detects nuclei and (e.g. PAS stained)
mucin. The App outputs area (µm2) of detected tissues/tissue classes, count of
total cells and in each detected area as well as the area of stained mucin in
the entire tissue and within the subclasses. Image Courtesy: Priv.-Doz.Dr.
Martin Schepelmann
App Category 2
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IHC SWISS ROLL
The IHC Swiss Roll App allows for detection of the swiss roll, and the
segmentation into different subclasses (mucosa, immune cell follicles,
connective tissue, background). Further it detects nuclei and identifies
phenotypes based on specific stains. The App outputs area (µm2) of detected
tissues/tissue classes, count of total cells as well as in each detected area.
Count and % of specific phenotype detected in total as well as in the tissue
classes. Image Courtesy: Priv.-Doz.Dr. Martin Schepelmann
App Category 2
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IF SWISS ROLL
The IF Swiss Roll App allows for detection of the swiss roll, and the
segmentation into different subclasses (mucosa, immune cell follicles,
connective tissue, background). Further it detects nuclei and identifies
phenotypes based on specific IF stains. The App outputs area (µm2) of detected
tissues/tissue classes, count of total cells as well as in each detected area.
Count and % of specific phenotype detected in total as well as in the tissue
classes. Image Courtesy: Priv.-Doz.Dr. Martin Schepelmann
App Category 2
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IHC INSULIN ISLETS
The IHC Insulin Islet App allows for detection of marker stained insulin islets,
the whole tissue, and cellular phenotypes stained by specific markers within the
insulin islets and in the tissue. The App outputs, whole tissue area (µm2),
number and area (µm2) of detected insulin islets. Number of cells and
marker-specific phenotypes in the whole tissue as well as within the insulin
islets.
App Category 2
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IHC ADIPOCYTES +
The IHC Adipocytes+ App identifies adipocytes and cellular aggregates inbetween
the adipocytes. Small rips in adipocyte membranes are mended automatically and
cell membrane artefacts in adipocyte lumina are automatically eliminated. The
App outputs number and area measurements for all detected adipocytes as well as
number and area of cellular aggregates.
App Category 2