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Pathology 218
Computational analysis of biological images Spring 2009 |
Lectures: Tuesdays 1:00-3:00pm Room L201 (Lane Building)
TA Office Hours
(for coding help) Fridays 3:30pm-5:00pm M327 on the 3rd floor of Alway.
Table of Contents
| Announcements |
Office hours will be moved back 1 hour this Friday to 3:30-5PM in M327.
Guidelines for presentations:
15 minutes for presentation followed by 5-10 minutes of discussion.
A suggested starting point: describe the overall project including:
-The background Biology
-Images (and how they were obtained)
-The goal of the image processing
Be sure to address the analysis methods you used.
Please be sure to show your raw images, intermediate figures if you think
they would be helpful, and describe your results.
Your choice as to whether you want to use presentation software (
powerpoint, acrobat or keynote) or just introduce the question (as above)
and describe the approach and results.... send us whatever you use for
your presentation along with your code.
Office hours have moved back to Fridays, 2:30-4:00PM in M327.
The schedule for presentations is as follows:
As a reminder, we have presentations in the 2 upcoming weeks:
May 26th
Matt
Carolina, Sandhya
Feng-Chiao
Elizabeth
Erik M
June 2
Erik L., Michael
Sonia
Johanna, Yin Loon
David, Drew, Kat, Lena
Weibin, Huibin
The notes have been posted for today's lecture. These also include the
schedule for the meetings for the project that have been set up. They will
be held in L332. Please bring your ideas for a project and sample
image(s).
In addition, these notes include details on the format of the written
proposal, due Thursday, 5/14 at 10PM.
Lecture notes from 4/28 are now online, along with the homework due at 11:54AM Pacific Daylight Time on Friday 5/8.
Tuesday's lecture notes and homework 4 are now posted, it is due Thursday, April 30th at 10PM. Accompanying images are posted as well. Remember to find an image that intersts you where you can count something. Please be sure to send in your assignment 3 due TODAY at 5PM .
We have posted the notes and assignment for last Tuesday. There is an image you will need to download as well (you will find it where the lecture is). The assignment won't be due until 5PM Pacific Daylight Time on Thursday 4/23.
In addition to the homework this week, please spend some time thinking of an image, either from your work or something published online, where it would be interesting to count some type of object such as animals, cells (in the figure from Tuesdays class for example), molecules, bands in a gel, etc.
TA office hours have been moved to Fridays, 2:30-4:00PM in M327. Please find corrections ot the problem set 2 in the updated version. The code is shown below for problems 7 and 8
7. Now retrace what we did in class, first we want the maximum and
minimum values for the red channel
int RMax=0;
int RMin=255;
int RCurrent=0;
for ( int y = 0; y < HEIGHT; y++ ) {
for ( int x = 0; x < WIDTH; x++ ) {
RCurrent=input1_raster.getSample(x,y,RED_BAND);
if (RCurrent> RMax) {RMax=RCurrent;}
if (RCurrent< RMin) {RMin=RCurrent;}
}
}
8. Then we want to normalize the sample based on these values
for ( int y = 0; y < HEIGHT; y++ ) {
for ( int x = 0; x < WIDTH; x++ ) {
RCurrent=input1_raster.getSample(x,y,RED_BAND);
if (RMax>RMin) {RCurrent=((RCurrent-RMin)*255)/(RMax-RMin);}
output1_raster.setSample(x,y,RED_BAND,RCurrent);
}
}
TA office hours will be kept on Fridays, and help will be available Tuesday
after class as well. Please email Sarah with any concerns.
Lecture notes and homework 2 have been posted. In addition, under
resources some Java references have been added.
A helpful way to keep track of brackets when coding is to indent your code
based on what level you are looking at. For example, the block under an if
statement should be indented more than the if statement itself. By having
a bracket on its own line you can simply line up the brackets. For
example:
if (statement you want)
{
perform some operations of statements...
for (some loop I want to execute)
{
nested operations to perform
}
}
Please download the updated homework with corrections ot the code in
question 7.The code should read:
output1_raster.setSample(x,y,RED_BAND,
255 - input1_raster.getSample(x,y,RED_BAND));
output1_raster.setSample(x,y,GREEN_BAND,
255 - input1_raster.getSample(x,y,GREEN_BAND));
output1_raster.setSample(x,y,BLUE_BAND,
255 - input1_raster.getSample(x,y,BLUE_BAND));
1) TA office hour locations have been set in the small half of the
genetics library, which is room M327 on the 3rd floor of Alway,
2:30-4:00 on Fridays.
2) We are requiring Java as the programming language for the course.
Molbench will be a great resource, as well as the java.sun.com
website. I will be available Fridays for help as well!
We have added updated version of Molbench under resources in addition to a Linux version. Please follow the directions carefully when installing the software on the Mac, as it contains a package to allow you to use .tif files.
Please send an email to Sarah if you are auditing the class to receive regular announcements.
| Homeworks |
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| March 31, 2009 | Lecture 1 UPDATED | due at 5PM Pacific Daylight Time on Wednesday 4/8 | P1 Sample Solutions |
| March 31, 2009 | Lecture 2 UPDATED | due at 5PM Pacific Daylight Time on Wednesday 4/15 | P2 Sample Solutions | April 16, 2009 | Lecture 3 Image |
due at 5PM Pacific Daylight Time on Thursday 4/23 | April 23, 2009 | Lecture 4 Image 1 Image of cells Image of worm muscle |
due at 10PM Pacific Daylight Time on Thursday 4/30 |
| May 1, 2009 | Lecture 5 | due at 11:54 AM Pacific Daylight Time on Friday 5/8 | |
| May 5, 2009 | Lecture 6 | Written proposals are due at 10 PM Pacific Daylight Time on Thursday 5/14 |
| Tentative List of Topics |
| General Course Information |
Andrew Fire:Teaching Assistant:
afire@stanford.edu
Tel:723-2885
Sarah Aerni
saerni@stanford.edu
Office Hours: (for coding help) Friday 3:30pm-5:00pm M327 on the 3rd floor of Alway
Course Goal:
Introduce students to the use of physical and computational tools to acquire, process, interpret, and archive biological images. Emphasis on digital microscopy as a tool and example.
Class Dates:
March 31, April 7,14,21,28; May 5,12,19,26 June 2
Lectures:
Informal introduction to concepts in this area, participatory discussion of critical analysis, and examples of applications.
Assignments:
Varying formats: Problem sets including coding of image manipulation routines. This is not a dedicated programming course, but students will learn to write and modify image analysis routines using the Java programming language.
Prerequisites:
Basic biomedical science background, no programming background is assumed. Optional introductory reading and review exercises will be provided for students with less extensive computation/microscopy experience.
Course Enrollment:
Limited enrollment-- Please email instructor if you are interested in -- -- enrolling.
| Course Resources |
Java Help Online
Great online Java quick reference guide:http://www.digilife.be/quickreferences/QRC/JAVA%20Quick%20Reference.pdf
http://www.digilife.be/quickreferences/quickrefs.htm
MolBench:
Updated Molbench (1.6):1. Download file and unzip - You will get a folder called MolbenchWindows Version
2. Move this folder to your applications folder
3. Move the jai_imageio.jar file into the folder /Library/Java/Extensions/
This folder is found by going to the top level (Hard drive) of the Mac system
4. Make sure that the name of the folder enclosing the Molbench application is "Molbench"
Please install as before. You will need to get a version of Java. These are available on the Sun websiteLinux
This may take a bit more work. You will need to install SUN JDK. Here are some instructions for that (untested)... for Ubuntu Linux http://www.cyberciti.biz/faq/howto-ubuntu-linux-install-configure-jdk-jre/Old versions:
Windows Version
Mac Version
Please contact Sarah with any problems
