Advanced image analysis
Automating your image processing
Getting useful information out of our image data often requires analysis with computer programs like Fiji/ImageJ. However, when we have very large amounts of data, or particularly complex analyses we need to be able to use those programs in more sophisticated ways. This course looks at ways to automate analyses and develop more complex processing tools.
Instructors
- Matthew Hartley
- Tjelvar Olsson
Audience
This course is aimed at those who either have substantial quantities of image data that they're interested in processing using automated methods, or those whose image analyses stretch the limits of what is possible in Fiji without developing custom analysis code or plugins.
Overview
Processing bioimage data often involves repetitive tasks. This can occur when there are lots of similar files to be processed, or certain processing steps need to be run lots of times. This course will look at ways to automate processing of images, including making macros and batch processing. We'll also look at what to do when the analyses we want aren't possible with standard tools, and we need to develop custom analyses, either by extending Fiji or using programming languages like Python.
Schedule
Day1
9:30 Start
11:30 Coffee break
12:30 End
Learning outcomes
By the end of the course you should be able to:
- Convert processing steps in Fiji into macros, and run these on sets of images
- Run simple Python scripts to process images
- Understand how programming and script development in Python or Fiji allows more flexible image analysis
Pre-requisites
This course assumes a good working knowledge of how to use Fiji for basic image processing.
Full course syllabus
- TBC
Course materials
Course book
Automating your image processing
Instructors
- Matthew Hartley
- Tjelvar Olsson
Audience
This course is aimed at those who either have substantial quantities of image data that they're interested in processing using automated methods, or those whose image analyses stretch the limits of what is possible in Fiji without developing custom analysis code or plugins.Overview
Processing bioimage data often involves repetitive tasks. This can occur when there are lots of similar files to be processed, or certain processing steps need to be run lots of times. This course will look at ways to automate processing of images, including making macros and batch processing. We'll also look at what to do when the analyses we want aren't possible with standard tools, and we need to develop custom analyses, either by extending Fiji or using programming languages like Python.Schedule
Day1
| 9:30 | Start |
| 11:30 | Coffee break |
| 12:30 | End |
Learning outcomes
By the end of the course you should be able to:- Convert processing steps in Fiji into macros, and run these on sets of images
- Run simple Python scripts to process images
- Understand how programming and script development in Python or Fiji allows more flexible image analysis
Pre-requisites
This course assumes a good working knowledge of how to use Fiji for basic image processing.Full course syllabus
- TBC