Assignment 2
Thank you!
Dr. Rudolph Pienaar
Fetal Neonatal Neuroimaging and Developmental Science Center
Today at 12pm
We are ready!
Everyone will present at least 1 paper this semester
You will work in a group of 3!
2-3 papers per Journal Club
Sign-up now!
The Rules
2-3 Papers per Session
Open and Flexible Format
Roughly 15-20 Minutes p.P.
Lead by Students
1. Explain the Story
2. Discuss the Paper
High-Level!
We are ready!
Everyone will present at least 1 paper this semester
You will work in a group of 3!
2-3 papers per Journal Club
Sign-up now!
it's all numb3rs but you need to figure out the conventions...
Image Filtering
Input
Output
Kernel
Thresholding
Input
Input > 200
Count
Color
everything < 200 set to 0
everything < 247 set to 0
Histogram
How to segment the tumor?
Binary segmentation mask
Segmentation
means dividing up an image into different structures
foreground vs. background
BG
FG
Label Map
each identified structure has a unique ID
Datatype?
Comparison of Segmentation Techniques
Automatic Segmentation is a hard problem!
so much variability across subjects!
Semi-Automatic Segmentation
user places seeds
Manual Segmentation or Expert Segmentation is the "Groundtruth"
extremely time-consuming
2 Experts worked on this for 6 months
Registration
Registration
a
b
c
Registration
Registration
mapping one subject to a standard space
mapping one image modality to a standard space
once in standard space, we can apply knowledge or compare
Atlas-based Segmentation
Registration / Alignment
Images are 2D Arrays!
2D Image Modalities
Ultrasound
X-Ray
What about CT, MRI, EM?
Image Volumes
Fetal MRI
2D
3D
Marching Cubes creates 3D Meshes
Bill Lorensen 1987
Label Maps
R.I.P.
Slice-based Volume Rendering
Volume Rendering with Ray Casting
Volume Rendering with Ray Casting
Single-click Interaction
CACTAS-Tool
Cinematic Volume Rendering
DICOM
Study
Patient
Series
2D Images
Picture archiving and communication system (PACS)
From DICOM...
...to .NRRD, .NIFTI, and others!
ton of converters available
