A SUITE OF WEB TOOLS FOR A SUITE OF WEB TOOLS FOR MORPHOMETRIC, GENETIC, AND MORPHOMETRIC, GENETIC, AND
MICROARRAY MICROARRAY ANALYSIS OF THE MOUSE CNSANALYSIS OF THE MOUSE CNS
Glenn Rosen, Melburn Park, Robert Glenn Rosen, Melburn Park, Robert Williams, Jonathan Nissanov, and Ken Williams, Jonathan Nissanov, and Ken
ManlyManly
Informatics Center for Mouse Informatics Center for Mouse NeurogeneticsNeurogenetics
• The Mouse Brain LibraryThe Mouse Brain Library - - RosenRosen
• iScopeiScope -Williams, Park -Williams, Park• NeurocartographerNeurocartographer - Nissanov - Nissanov• Neurogenetics Tool BoxNeurogenetics Tool Box - -
ManlyManly
Goal of ProjectGoal of Project
• Provide online resource for Provide online resource for complete mapping of complete mapping of differences in brain structure differences in brain structure to defined sets of genes to defined sets of genes (quantitative train loci; QTLs)(quantitative train loci; QTLs)
• Large scale (e.g., brain weight, Large scale (e.g., brain weight, volume)volume)
• Small scale (e.g., neuron number)Small scale (e.g., neuron number)
Specfic ImplementationSpecfic Implementation
• Universal Access to Universal Access to Neuroanatomic PhenotypesNeuroanatomic Phenotypes
• Digital DissectionDigital Dissection• Comprehensive Genotype Data Comprehensive Genotype Data
and Tools for Complex Trait and Tools for Complex Trait AnalysisAnalysis
Universal Access to Universal Access to Neuroanatomic PhenotypesNeuroanatomic Phenotypes
• The Mouse Brain LibraryThe Mouse Brain Library• Digital images (0.1–25 µm/pixel) from Digital images (0.1–25 µm/pixel) from
inbred, RI, and advanced intercross inbred, RI, and advanced intercross mice.mice.
• Ideal for stereologic analysis.Ideal for stereologic analysis.
• iScopeiScope• High-power, through-focus movies.High-power, through-focus movies.• Microscope controlled over the internet.Microscope controlled over the internet.• Ability to perform neuronal counts on Ability to perform neuronal counts on
selected regions of selected sections.selected regions of selected sections.
Digital DissectionDigital Dissection
• NeurocartographerNeurocartographer• Generate 3D atlas of mouse brain.Generate 3D atlas of mouse brain.• Use 3D atlas to automatically Use 3D atlas to automatically
segment regions of brain.segment regions of brain.
Comprehensive Genotype DataComprehensive Genotype Data
• DatabasesDatabases• RI genotypes and phenotypesRI genotypes and phenotypes• Advanced intercross progeny (GAdvanced intercross progeny (G1010))• Microarray data from inbred and RI Microarray data from inbred and RI
strainsstrains
• Neurogenetic Tool BoxNeurogenetic Tool Box• QTLs without tissue or DNA (WebQTL)QTLs without tissue or DNA (WebQTL)• Statistically evaluate neuroanatomic Statistically evaluate neuroanatomic
and microarray data with these DBsand microarray data with these DBs
The Mouse Brain The Mouse Brain LibraryLibrary
Gene Discovery by QTL Gene Discovery by QTL MappingMapping
•Quantitative Trait LociQuantitative Trait Loci
• Many medically interesting traits are complex Many medically interesting traits are complex traitstraits
• Complex = multiple genes and non-genetic Complex = multiple genes and non-genetic factorsfactors
• Genes which control complex traits are QTLsGenes which control complex traits are QTLs
•QTLs are detected by statistical associationsQTLs are detected by statistical associations
• Trait values Trait values marker locus genotypes (or marker locus genotypes (or estimated genotypes between markers)estimated genotypes between markers)
• Potential QTL indicated by LOD score maximumPotential QTL indicated by LOD score maximum
• Significance measured by LOD score valueSignificance measured by LOD score value
QTL Mapping PrinciplesQTL Mapping Principles
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TraitMarker genotype
Pro
geny
indi
vidu
als
Evaluate association for many markers and locations between markers
map location
sign
ific
ance
QTL Mapping GoalsQTL Mapping Goals
• SignificanceSignificance• Which LOD score maxima Which LOD score maxima
correspond to statistically correspond to statistically significant QTLs?significant QTLs?
• LocationLocation• How precisely does the LOD How precisely does the LOD
score maximum define the QTL score maximum define the QTL location? location?
• ArchitectureArchitecture• How many QTLs and what How many QTLs and what
interactions determine a interactions determine a particular trait?particular trait?
Permutation Test for Permutation Test for SignificanceSignificance
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TraitTraitMarker Marker
genotypegenotype
P = 0.05
LRS statistics from 1000 LRS statistics from 1000 regressions with permuted regressions with permuted
datadata
Bootstrap for LocationBootstrap for Location
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TraitMarker genotype
.
. 200 repetitions
.
Lateral VentriclesLateral Ventricles
Distribution of Ventricle SizeDistribution of Ventricle Size
0
1
2
3
4
Per
cent
Ven
tric
le
A/J
C57
BL /
6J
AX
B4
BX
A8
BX
A7
BX
A4
AX
B8
AX
B6
BX
A17
AX
B15
AX
B5
BX
A16
BX
A14
AX
B13
AX
B20
AX
B12
BX
A2
BX
A12
BX
A1
BX
A13
BX
A11
BX
A24
BX
A25
AX
B10
AX
B2
BX
A26
AX
B1
AX
B24
Strain
Mapping Ventricle SizeMapping Ventricle Size
0
5
10
15
20
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 X
LR
S S
core
LR
S S
core
ChromosomeChromosome
Epistatic InteractionsEpistatic Interactions
The iScopeThe iScope
Two Goals for the Online Two Goals for the Online MicroscopeMicroscope
• Web publication of Web publication of hardhard slide slide librarieslibraries• MBLMBL• Pathfinding for other collectionsPathfinding for other collections
• Automatic production of Automatic production of softsoft librarieslibraries
Java InterfaceJava Interface
• Navigation Navigation controlscontrols
• High and low High and low power index power index viewsviews
• Quicktime Quicktime screenscreen
Control PaneControl Pane
Navigation PanesNavigation Panes
• Blue crosshairs Blue crosshairs show current show current locationlocation
• Moveable red Moveable red dot selects dot selects desired locationdesired location
SchedulingScheduling
Co-development: Focussing Co-development: Focussing ProblemProblem
• Automatic focussing via Automatic focussing via proprietary noise-analysis proprietary noise-analysis algorithmalgorithm
• Interaction with vendor to Interaction with vendor to obtain custom chip giving us obtain custom chip giving us software access to noise valuesoftware access to noise value
• Focussing can be taken on- of Focussing can be taken on- of off-board off-board
Robotic Slide LibraryRobotic Slide Library
• Commercial Commercial designdesign
• Smartmotor™ Smartmotor™ technologytechnology
• Pneumatic Pneumatic actuatorsactuators
• Changeable Changeable cassettescassettes
• 6x82 2x3 inch 6x82 2x3 inch slidesslides
NeurocartographerNeurocartographer
The Navigation ProblemThe Navigation Problem
TT
T
T
T
Atlas (C57BL/6J Male)Atlas (C57BL/6J Male)
• www.neuroterrain.orgwww.neuroterrain.org• www.www.nervenetnervenet.org.org
Atlas AvailabilityAtlas Availability
2D-2D Rigid-body Alignment
BlockfaceImages
SectionImages
Median Filter
AIR
Error Detection
Reinitiali-zation
AIR
Acceptable? Resample
Reconstruction
SectionImages
Alignment Parameters
Y
N
MacroVoxel ArchitectureMacroVoxel Architecture
NetworkConnectionNetworkSlicingEngine
AtlasViewNavigation
ControlVOI Display
ManagementMouse
TrackingMovement controlsSlicing Axis controlTrack resultsReturned imageReslicecommandsVOI displayparameters
Neurocartographer ClientNetworkConnectionSlicingEngineAtlasData
Model
K2 CommandRedirection
ClientParameterSupport
Reslice commandClient displaysettings
K2 controlsclient displayNeurocartographer ServerK2 softwareNetworkConnection
DatabaseConnectionFederationImage data accessMetadata
access
Server-Client MacOStatServer-Client MacOStat
Ordered Unaligned 2D 2.5D
Auto Manual
Matching Plane Pairs
Matching Inplane Features
3D Reconstruction
Aligned Sections
Auto Manual
Z-A
xis
mat
chin
gX
Y P
lane
mat
chin
gW
arpi
ng
Matching 3D Features
3D
ParcellationParcellation
WarpingWarping
refere
nce
test
test
Case 1:
Case 2:
ResultsResultsCase 1 Case 2
Next StepNext Step
Neurogenetics Tool Box Neurogenetics Tool Box (WebQTL)(WebQTL)
WebQTLWebQTL
Trait data from MouseBrain Library images
UsersTrait data from
Neurocarto-grapher
User traitdata
Trait data from MouseBrain Library images
UsersTrait data from
Neurocarto-grapher
User traitdata
WebQTL Mapping ServiceWebQTL Mapping Service• http://http://
webqtl.roswellpark.org/webqtl.roswellpark.org/• Mapping populationsMapping populations
• Recombinant inbred linesRecombinant inbred lines• BxD advanced intercrossBxD advanced intercross
• No genotyping necessaryNo genotyping necessary
WebQTL Data EntryWebQTL Data Entry
• Choice of data entry Choice of data entry methodsmethods• Choose a data fileChoose a data file• Paste or type dataPaste or type data
WebQTL Data ConfirmationWebQTL Data Confirmation• Data entry or Data entry or
confirmation formconfirmation form
Mapping ProceduresMapping Procedures
Interval MappingInterval Mapping
Interval Mapping DetailInterval Mapping Detail
Future DirectionsFuture Directions
• MBLMBL• Extend MBLExtend MBL• Improve DB integrationImprove DB integration• Interface enhancementInterface enhancement• On-line image analysis On-line image analysis
toolstools
• iScopeiScope• Additional design and Additional design and
constructionconstruction• Robotic slide handlingRobotic slide handling• Web archive of through-Web archive of through-
focus image stacksfocus image stacks• Streaming VideoStreaming Video
• NeurocartographerNeurocartographer• Strengthen and extend Strengthen and extend
segmentation algorithmsegmentation algorithm• Segment MBLSegment MBL
• Neurogenetics Tool Neurogenetics Tool BoxBox• Batch submission of Batch submission of
multiple traitsmultiple traits• Search for interacting Search for interacting
QTLsQTLs• Data archiving and exportData archiving and export• Additional crosses and Additional crosses and
cross designscross designs• DNA ArrayDNA Array
AcknowledgmentsAcknowledgments
• This project is part of the Human Brain Project/Neuroinformatics program funded jointly by the National Institute of Mental Health, National Institute on Drug Abuse, and the National Science Foundation (P20-MH 62009).
MBL Intro
MBL BD
Mbl Small
MBL All
Slide
MBL High
Power