BIP_ProjectAssignment_01_S2023_INSTRUCTIONS.pdf

Zixin Huo

2页

1次

2023-04-05

10墨值下载

Biological Image Processing and Informatics

Spring 2023

Project Assignment #1

Assigned on MAR-16-2023

Due on APR-06-2023 by 10pm @Education Cloud

A. Overview

This assignment reviews some basic operations in image analysis and computer vision, such as reading/writing

of an image, displaying an image, calculating the intensity histogram of an image, and defining a region-of-

interest, and image segmentation.

NOTE: Each student is required to complete this assignment individually.

Please install a copy of ImageJ for viewing images for this project. You may also find it useful to install a copy

of IrfanView or comparable image viewer software that can handle 16-bit images.

For this assignment, we ask you to use MATLAB or Python. The total score for this assignment is 60 points +

10 points extra credit.

B. Questions

Question 1 (20 points): Basic concepts of image analysis and computer vision

Part I: If you choose MATLAB, we ask you to use the MATLAB Image Processing Toolbox. If you choose

to use Python, we suggest the Pillow package (https://pillow.readthedocs.io/en/stable/), Scitkit-image

(https://scikit-image.org/) or OpenCV (https://opencv.org/).

We ask you to familiarize yourself with either the Image processing Toolbox or the Pillow

package and answer the following questions

- What are the image formats supported?

- How to read, display, and write an image?

- Please give a summary of the image processing functions provided.

Question 2 (20 points): Input/output of a static greyscale image

2.0 Download the image named “axon01.tif” from Education Cloud.

2.1 Read the image using MATLAB or Python and display it. Write a program to plot its intensity histogram.

Please do NOT use the build-in image intensity histogram function. Instead, please write your own image

intensity histogram code by calling the histogram function in MATLAB or Python. (10 points)

2.2 Write a program to define a rectangular region of interest (ROI), crop the image within the ROI and save

the cropped image in a non-compressed TIF format (please feel free to assign a name for the saved image). (10

points)

Question 3 (20 points): Image segmentation using ICY-Spot Detector

3.0 Download and install a copy of ICY-Spot Detector (http://icy.bioimageanalysis.org)

3.1 Use the program to segment the image named “axon01.tif”. Show your result.

Question 4 (EXTRA CREDIT: 10 points): Retrieving image from

4.0 Retrieve an image of mitochondria from Protein Atlas, specifically the Cell Atlas (5 points）.

https://www.proteinatlas.org/

4.1 Use the ICY(select a segmentation toolbox) or CellProfiler (https://cellprofiler.org/) to segment the

retrieved image as well as “axon02.tif” and “cell_nucleus.tif” (5 points).

C. Instructions on report writing

1) Write a project report in either Chinese or English following the format listed below.

Submit the report in hard copy.

The report should include the following sections:

– Project number and title, student name, date of submission

– Introduction: write a general and brief summary of the project.

– Code execution instruction: provide clear instructions on how to run your code.

– Result section: present key results by showing the images. This part should be organized largely

following the sequence of questions. Concisely explain/comment on your results.

– Summary/discussion section: summarize and discuss what you have learned from this project.

– References: list references you want to cite.

2) As a requirement for best practice in programming, your code should be properly formatted and

commented.

3) Submit relevant images generated for this assignment. See instructions below.

D. Instructions on report submission

- For this assignment, report submission will be handled by Education Cloud.

- Package all programs and results files (e.g. videos) into one file using any of the commonly used

compression software (WinZip, WinRAR, etc). Be sure to include your name in the file name.

E. Report format

There is no page limit for the project report.

Page size: letter

Line space: single

Page margins: 0.5 inch on each side (top, bottom, left, right)

Font size: 11 or 12 points font for the main text; 10 points for listed references