TMS016 / MSA301 Spatial statistics and image analysis
This page contains the program of the course: lectures and computer labs. Other information, such as learning outcomes, teachers, literature and examination, are in a separate course PM.
Program
The schedule of the course is in TimeEdit.
The course has two lectures and two computer exercises each week. Details for these are given in the schedule below, which will be updated during the course. For the lectures, the chapters covered in the books are listed, where LN denotes the lecture notes by Mats Rudemo, HS denotes the Handbook of spatial statistics and EL The Elements of Statistical Learning.
The lectures will be given in Euler but it is also possible to follow them on Zoom using the link https://chalmers.zoom.us/j/61569881002, Password: 642830
Projects and examination
The deadlines for the projects can be found in the end of this page under Course summary. The reports should be uploaded in Canvas/Assignments.
In addition to the projects, there will be a final exam on June 1 at 14:00-18:00.
Lectures and Exercises
Teachers of the course are Aila Särkkä (lectures, examiner), aila@chalmers.se, and Konstantinos Konstantinou (lectures, computer exercises), konkons@chalmers.se. Lecture notes of the lectures can be found in Files/Lecture notes. The information below will be updated and extended on an ongoing basis.
| Time | Room | Lecture | Computer exercise | ||
|---|---|---|---|---|---|
| March 21 | Monday 8:00-9:45 |
Euler | L1 |
Introduction, lecture notes and LN pages 1-24, see also pages 1-8 of Glasbey and Horgan 1995, Chapter 5. |
|
| Monday 13:15-15:00 |
MVF24 and MVF25 | E1 | |||
| March 23 | Wednesday 10:00-11:45 |
Euler | L2 | Spatial random processes, lecture notes and LN pages 69-78. | |
| Wednesday 13:15-15:00 |
MVF24 and MVF25 | E2 | |||
| March 28 | Monday 8:00-9:45 |
Euler | L3 |
OLS, GLS and ML estimation, lecture notes and LN pages 78-85. |
|
| Monday 13:15-15:00 |
MVF24 and MVF25 | E3 | |||
| March 30 | Wednesday 10:00-11:45 |
Euler | L4 |
GMRFs, HS pages 172-175, 201-207. LDA, QDA, image moments, LN pages 31-38 and EL 4.3 |
|
| Wednesday 13:15-15:00 |
MVF24 and MVF25 | E4 | Continue working on exercise 3 | ||
| April 4 | Monday 8:00-9:45 |
Euler | L5 |
Cross validation, supervised methods, LN pages 38-42 and 53-59 and sections 2.3.2, 7.10, 12.2-12.3.2, 11.3-11.5 in EL |
|
| Monday 13:15-15:00 |
MVF24 and MVF25 | E5 | |||
| April 6 | Wednesday 10:00-11:45 |
Euler | L6 |
Image segmentation, morphological operations and feature extraction. LN 1.5-1.6, 2.8. See also EL 8.5.1, 14.3.6-14.3.7. |
|
| Wednesday 13:15-15:00 |
MVF24 and MVF25 | E6 | |||
| April 25 | Monday 8:00-9:45 |
Euler | L7 | Markov random fields, lecture notes and LN pages 60-67 | |
| Monday 13:15-15:00 |
MVF24 and MVF25 | E7 | |||
| April 27 | Wednesday 10:00-11:45 |
Euler | L8 | Point process analysis, lecture notes LN pages 86-93. | |
| Wednesday 13:15-15:00 |
MVF24 and MVF25 | E8 | |||
| May 2 | Monday 8:00-9:45 |
Euler | L9 |
Marked point processes, point processes with noise, lecture notes and LN pages 94-96 and 117-129. |
|
| Monday 13:15-15:00 |
MVF24 and MVF25 | E9 | |||
| May 4 | Wednesday 10:00-11:45 |
Euler | L10 | Applications of point processes/image analysis to nerve fiber data, lecture notes |
|
| Wednesday 13:15-15:00 |
MVF24 and MVF25 | E10 | Point processes | ||
| May 9 | Monday 8:00-9:45 |
Euler | L11 | Guest lecture on analysing microscopy (FIB-SEM, FRAP, and particle tracking) data by Magnus Röding, RISE, lecture notes | |
| Monday 13:15-15:00 |
MVF24 and MVF25 | E11 | Work on projects | ||
| May 11 | Wednesday 10:00-11:45 |
Euler | L12 | Analysing microscopy data by RICS and SPRIA, lecture notes and LN pages 145-153 | |
| Wednesday 13:15-15:00 |
MVF24 and MVF25 | E12 | Work on projects | ||
| May 16 | Monday | Work on projects | |||
| May 18 | Wednesday | Work on projects | |||
| May 23 | Monday 8:00-9:45 | Euler | L13 | Project seminars | |
| Monday 13:15-15:00 |
Euler | E13 | Project seminars | |
|
| May 25 | Wednesday 10:00-11:45 |
Euler | L14 | Project seminars | |
| Wednesday 13:15-15:00 |
Euler | E14 | Project seminars |
Computer labs
The exercises will be done in Matlab, and some knowledge of Matlab is assumed. If you need an introduction, see Learning MATLAB, Tobin A. Driscoll ISBN: 978-0-898716-83-2 (The book is published by SIAM).
Most computer exercises will use functions written specifically for this course. These are collected in the following file: TMS016_Matlab.zip. Download this file and add the path to the folder in matlab: addpath('path_to_folder'). Then run the command tms016path to set the path to the files.
Data used in the exercies are colleded here: TMS016_Data.zip.
Reference literature:
Learning MATLAB, Tobin A. Driscoll ISBN: 978-0-898716-83-2 (The book is published by SIAM).
Course summary:
| Date | Details | Due |
|---|---|---|