Daniel Haehn PRO
Hi, I am a biomedical imaging and visualization researcher who investigates how the study of brain connectivity and machine perception can help advance the understanding of biologically inspired artificial intelligence.
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
CS666 Lecture 16
By Daniel Haehn
CS666 Lecture 16
Slides for CS666 Biomedical Signal and Image Processing at UMass Boston. See https://cs666.org!
