1. A SUITE OF WEB TOOLS FOR MORPHOMETRIC, GENETIC, AND MICROARRAY ANALYSIS OF THE MOUSE CNS Glenn Rosen, Melburn Park, Robert Williams, Jonathan Nissanov, and Ken Manly

2. Informatics Center for Mouse Neurogenetics The Mouse Brain Library - RosenThe Mouse Brain Library - Rosen iScope -Williams, ParkiScope -Williams, Park Neurocartographer - NissanovNeurocartographer - Nissanov Neurogenetics Tool Box - ManlyNeurogenetics Tool Box - Manly

3. Goal of Project Provide online resource for complete mapping of differences in brain structure to defined sets of genes (quantitative train loci; QTLs)Provide online resource for complete mapping of differences in brain structure to defined sets of genes (quantitative train loci; QTLs) Large scale (e.g., brain weight, volume)Large scale (e.g., brain weight, volume) Small scale (e.g., neuron number)Small scale (e.g., neuron number)

4. Specfic Implementation Universal Access to Neuroanatomic PhenotypesUniversal Access to Neuroanatomic Phenotypes Digital DissectionDigital Dissection Comprehensive Genotype Data and Tools for Complex Trait AnalysisComprehensive Genotype Data and Tools for Complex Trait Analysis

5. Universal Access to Neuroanatomic Phenotypes The Mouse Brain LibraryThe Mouse Brain Library Digital images (0.1–25 µm/pixel) from inbred, RI, and advanced intercross mice. Digital images (0.1–25 µm/pixel) from inbred, RI, and advanced intercross 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 selected regions of selected sections. Ability to perform neuronal counts on selected regions of selected sections.

6. Digital Dissection NeurocartographerNeurocartographer Generate 3D atlas of mouse brain. Generate 3D atlas of mouse brain. Use 3D atlas to automatically segment regions of brain. Use 3D atlas to automatically segment regions of brain.

7. Comprehensive Genotype Data DatabasesDatabases RI genotypes and phenotypes RI genotypes and phenotypes Advanced intercross progeny (G 10 ) Advanced intercross progeny (G 10 ) Microarray data from inbred and RI strains Microarray data from inbred and RI strains Neurogenetic Tool BoxNeurogenetic Tool Box QTLs without tissue or DNA (WebQTL) QTLs without tissue or DNA (WebQTL) Statistically evaluate neuroanatomic and microarray data with these DBs Statistically evaluate neuroanatomic and microarray data with these DBs

8. The Mouse Brain Library

9. Gene Discovery by QTL Mapping Quantitative Trait Loci Quantitative Trait Loci Many medically interesting traits are complex traits Many medically interesting traits are complex traits Complex = multiple genes and non-genetic factors Complex = multiple genes and non-genetic factors Genes which control complex traits are QTLs Genes which control complex traits are QTLs QTLs are detected by statistical associations QTLs are detected by statistical associations Trait values  marker locus genotypes (or estimated genotypes between markers) Trait values  marker locus genotypes (or estimated genotypes between markers) Potential QTL indicated by LOD score maximum Potential QTL indicated by LOD score maximum Significance measured by LOD score value Significance measured by LOD score value

10. QTL Mapping Principles ABAABABB...ABAABABB... 12 18 13 10 17 11 19 20... Trait Marker genotype Progeny individuals Evaluate association for many markers and locations between markers map location significance

11. QTL Mapping Goals SignificanceSignificance Which LOD score maxima correspond to statistically significant QTLs? Which LOD score maxima correspond to statistically significant QTLs? LocationLocation How precisely does the LOD score maximum define the QTL location? How precisely does the LOD score maximum define the QTL location? ArchitectureArchitecture How many QTLs and what interactions determine a particular trait? How many QTLs and what interactions determine a particular trait?

12. Permutation Test for Significance ABAABABB...ABAABABB...ABAABABB...ABAABABB... 12 18 13 10 17 11 19 20... Trait Marker genotype P = 0.05 LRS statistics from 1000 regressions with permuted data

13. Bootstrap for Location ABAABABB...ABAABABB... 12 18 13 10 17 11 19 20... Trait Marker genotype.. 200 repetitions.

14. Lateral Ventricles

15. Distribution of Ventricle Size 0 1 2 3 4 P e r c e n t V e n t r i c l e Strain

16. Mapping Ventricle Size 0 5 10 15 20 12345678910111213141516171819X LRS Score Chromosome

17. Epistatic Interactions

18. The iScope

19. Two Goals for the Online Microscope Web publication of hard slide librariesWeb publication of hard slide libraries MBL MBL Pathfinding for other collections Pathfinding for other collections Automatic production of soft librariesAutomatic production of soft libraries

20. Java Interface Navigation controlsNavigation controls High and low power index viewsHigh and low power index views Quicktime screenQuicktime screen

21. Control Pane

22. Navigation Panes Blue crosshairs show current location Moveable red dot selects desired location

23. Scheduling

24. Co-development: Focussing Problem Automatic focussing via proprietary noise-analysis algorithmAutomatic focussing via proprietary noise-analysis algorithm Interaction with vendor to obtain custom chip giving us software access to noise valueInteraction with vendor to obtain custom chip giving us software access to noise value Focussing can be taken on- of off- boardFocussing can be taken on- of off- board

25. Robotic Slide Library Commercial designCommercial design Smartmotor™ technologySmartmotor™ technology Pneumatic actuatorsPneumatic actuators Changeable cassettesChangeable cassettes 6x82 2x3 inch slides6x82 2x3 inch slides

27. Neurocartographer

28. The Navigation Problem

29. T T T T T

30. Atlas (C57BL/6J Male)

31. www.neuroterrain.orgwww.neuroterrain.orgwww.neuroterrain.org www.nervenet.orgwww.nervenet.orgwww.nervenet.org Atlas Availability

32. 2D-2D Rigid- body Alignment Blockface Images Section Images Median Filter AIR Error Detection Reinitiali- zation AIR Acceptable? Resample Reconstruction Section Images Alignment Parameters Y N

33. MacroVoxel Architecture

34. Server-Client MacOStat

35. Ordered Unaligned 2D 2.5D Auto Manual Matching Plane Pairs Matching Inplane Features 3D Reconstruction Aligned Sections Auto Manual Z-Axis matching XY Plane matching Warping Matching 3D Features 3D

36. Parcellation

37. Warping reference test Case 1: Case 2:

38. Results Case 1Case 2

39. Next Step

40. Neurogenetics Tool Box (WebQTL)

41. WebQTL

42. WebQTL Mapping Service http://webqtl.roswellpark.org/http://webqtl.roswellpark.org/ Mapping populationsMapping populations Recombinant inbred lines Recombinant inbred lines BxD advanced intercross BxD advanced intercross No genotyping necessaryNo genotyping necessary

43. WebQTL Data Entry Choice of data entry methodsChoice of data entry methods Choose a data file Choose a data file Paste or type data Paste or type data

44. WebQTL Data Confirmation Data entry or confirmation formData entry or confirmation form

45. Mapping Procedures

46. Interval Mapping

47. Interval Mapping Detail

48. Future Directions MBLMBL Extend MBL Extend MBL Improve DB integration Improve DB integration Interface enhancement Interface enhancement On-line image analysis tools On-line image analysis tools iScopeiScope Additional design and construction Additional design and construction Robotic slide handling Robotic slide handling Web archive of through-focus image stacks Web archive of through-focus image stacks Streaming Video Streaming Video NeurocartographerNeurocartographer Strengthen and extend segmentation algorithm Strengthen and extend segmentation algorithm Segment MBL Segment MBL Neurogenetics Tool BoxNeurogenetics Tool Box Batch submission of multiple traits Batch submission of multiple traits Search for interacting QTLs Search for interacting QTLs Data archiving and export Data archiving and export Additional crosses and cross designs Additional crosses and cross designs DNA Array DNA Array

49. Acknowledgments 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).

51. MBL Intro

52. MBLBDMBLBD

53. Mbl Small

54. MBL All Slide

55. MBL High Power