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Image Analysis Algorithms

Supported by New York State Stem Cell Science


(NYSTEM)
For more information visit: Stemcell.ny.gov

Brightfield
Positive Pixel
Count
Color
Deconvolution

Calculates the contribution of each stain at


every pixel location in the image.
Separates the image into different layers,
corresponding to your stains.

Cytoplasmic
Staining

Measures intensity and provides the percentage


of cells containing stain.

Membrane
Analysis

Detects membrane staining for individual cells


and identifies the intensity and completeness of
the staining.

Nuclear
Analysis

The Stem Cell Pathology Unit


5cm tall

Detects nuclear staining, and intensity.

Microvessel
Analysis

Detects and quantifies microvessels stained


with endothelial markers.

Rare Event
Detection

The algorithm uses color segmentation and


morphological image processing methods to
detect and count objects of interest.

Fluoresce
nt
Cyto-Nuclear
FL

Designed to measure both cytoplasmic and


nuclear intensity on a cell-by-cell basis.

Object
Colocalization
FL

Capable of measuring object properties &


determining colocalized objects.

Microvessel FL

Designed to count vessels & measure vessel


properties.

Area
Quantification

Quantifies multiple florescent dyes on an area


basis.

Contact Information
The Director of the Stem Cell Pathology Unit:
Alexander Nikitin, MD, PhD
Professor of Pathology
Pathology:
Andrew Miller, DVM, Dipl. ACVP
Assistant Professor
adm10@cornell.edu
Teresa Southard, DVM, Dipl. ACVP, PhD
Assistant Clinical Professor
tls93@cornell.edu
Slide Digitization:
Chris Pelletier, Research Support Specialist
clp83@cornell.edu
For General Questions and Additional Information:
Website: stemcell.cornell.edu/PathUnit
Email: pathunit@cornell.edu

10.5cm wide

Animal Phenotyping
We offer comprehensive animal phenotyping with
a focus on the assessment of stem cell niches. Stem
Cell Pathology is a rapidly emerging discipline that
provides critical links between animal modeling,
intravital, and histopathological analysis. We
investigate
the
consequences
of
genetic
manipulation in stem cells and determine the roles of
stem cells in regenerative medicine and in the
pathogenesis of various diseases, such as cancer.
Our goal is to foster interdisciplinary collaboration
to facilitate the advancement of stem cell research.
The Cornell University Stem Cell Pathology Unit
provides comprehensive pathology services and
planning advice for all projects, with an expert focus
on stem cell related projects.
Project Planning
Our pathologists offer advice on the selection of the
most appropriate animal strains and tissue fixatives
suitable for your particular studies. When you are in the
process of experimental design, we can help you select
or design the most appropriate genetically modified
animals for your needs and offer our advice on the most
beneficial necropsy for comparative analysis.
Pathological Assessment
The assessment of disease pathogenesis by trained
pathologists is critical for stem cell research. We offer
the expertise to help you identify anatomically localized
stem cell niches during disease initiation and
progression. Our Stem Cell Pathology Unit combines
comprehensive animal phenotyping services with the
specialized assessment of stem cell niches.
Interdisciplinary Collaboration

For more information, please visit our website at:


website at:
stemcell.cornell.edu/PathUnit

For more information, please visit our


stemcell.cornell.edu/PathUnit

Various topics in regenerative medicine, such as the


in situ contributions of stem cells to normal and
pathologic regeneration, or organismal reactions to the
transplantation of various bioengineered constructs,
require the support of dedicated pathologists. Our
Pathology
Services
can
give
you
accurate
interpretations of novel findings and help with the
validation of model systems.

Pathology Services

We work closely with investigators to determine the


optimal sets of tissues to be examined in each animal.
Please email us regarding pricing for other animal models.

4cm tall
10.5cm wide

Cornell
Faculty

Whole Slide Digital Imaging & Analysis


Murine necropsy & tissue
collection (no histopath)

$80
/animal

Complete murine necropsy


(includes histopath up to 12 H&E
slides with final report)*

$250
/animal

Complete necropsy of wild-type


littermates

$100
/animal

Embryo evaluation up to GD 11
(requires parallel evaluation of
wild-type littermate)

$100
/embryo

Embryo/Fetus evaluation after to


GD 11 (requires parallel
evaluation of wild-type
littermate)

$150
/embryo

Histopathology slide review with


report, 1-2 slides

$50
/slide

Histopathology slide review with


report, 3 or more slides

$35
/slide

Histopathology review with


report generation

$150
/hr

Slide consultation, no report

$20
/slide

*Murine necropsy for phenotyping will include collection


of the following tissues: Heart, tongue, thymus, thyroid
gland, lymph nodes, salivary glands, lung, trachea,
esophagus, heart, liver, spleen, kidneys, adrenal glands,
ovaries/testes
and
epididymides,
uterus
and
vagina/prostate, seminal vesicles, coagulating glands and
bulbourethral glands, clitoral gland/preputial gland, urinary
bladder, urethra, mammary glands, stomach, duodenum,
pancreas, jejunum, ileum, cecum, colon, skin, brain and
pituitary gland, eyes, Harderian glands, bone, bone
marrow, teeth, pharynx, nasal cavity. Spinal cord/vertebral
column upon request.

The Stem Cell Pathology Unit offers digital


slide preparation for both brightfield and
fluorescent samples. To keep costs low, we train
users to scan their own slides. Image viewing
software, image analysis algorithms and 1
month of image storage are free for registered
users.

Preparation of Digital Slides

Leica ScanScopes capture precise high-resolution


slide images (eSlides) of brightfield, fluorescent, and
FISH specimens on glass slides. eSlides give you a
field of view that encompasses your entire tissue of
interest, instead of the small area you would
generate with a conventional slide.
Slides are scanned at giga-pixel resolutions
Brightfield eSlides are 24-bit color, up to a 40X
magnification
Fluorescent eSlides can have up to 4 channels, up
to a 40X magnification
Whole slide image analysis

Slide Scanning

For more information, please visit our website at:


website at:
stemcell.cornell.edu/PathUnit

Cornell Faculty
For more information, please visit our
stemcell.cornell.edu/PathUnit

$50/hr 8AM-8PM M-F


Bright-field
ScanScope
Fluorescen
t

$25/hr 8PM-8AM Nights &


Weekends

ScanScope
New User
Training

$70/hr 8AM-8PM M-F

For more information, please visit our website at:


website at:
stemcell.cornell.edu/PathUnit

$35/hr 8PM-8AM Nights &


Weekends
$100/Training Session

For scanning batches of slides,


please contact us for rates.

For more information, please visit our


stemcell.cornell.edu/PathUnit