Image analysis courses

Our regular half day image analysis training workshops are currently suspended due to Covid-19 but online versions are available.  Both ImageJ/Fiji Level 1 and 2 courses can be viewed on YouTube and the full lecture materials for all courses (ImageJ/Fiji, CellProfiler and MATLAB) are available via GitHub

 

ImageJ/Fiji Level 1: Basics of image processing and analysis

The workshop begins with a presentation introducing fundamental concepts of image analysis, characteristics of image data, its processing and segmentation. The attendees then learn how to use ImageJ/Fiji to analyse features in microscopy images by carrying out a series of hands-on exercises using provided images.  Examples concentrate on fluorescence microscopy, but the techniques used are widely applicable to other types of images.

- Lecture materials on GitHub (slides, worksheets and example data)
Video lecture (part 1) on YouTube
Video lecture (part 2) on YouTube

ImageJ/Fiji Level 2: Automation and batch processing using macros

The workshop includes a presentation introducing fundamental concepts of programming with a specific emphasis on the ImageJ macro language. Attendees will then learn how to run an automated image processing and segmentation routine on microscopy images by carrying out a series of hands-on exercises using provided images.

This workshop is suitable for anyone acquiring microscopy data as part of their research. Familiarity with ImageJ/Fiji will be necessary; particularly, content covered in the ImageJ/Fiji Level 1 course. ‚Äč   No prior knowledge of programming is necessary.

- Lecture materials on GitHub (slides, worksheets and example data)
Video lecture (part 1) on YouTube
Video lecture (part 2) on YouTube

CellProfiler: An introduction to object detection, measurement and batch processing 

CellProfiler is a free, open-source image analysis software package specialising in object segmentation and measurement. Processing steps are inserted as modules into workflow 'pipelines', which can be run in batch mode on image collections, with results collated into a single spreadsheet. Available CellProfiler modules include object segmentation, object size/shape measurement, object intensity measurement, colocalisation and spatial proximity/overlap of objects.

This workshop is suitable for anyone acquiring microscopy data as part of their research. Familiarity with basic image processing concepts will be necessary. These concepts are covered in the ImageJ/Fiji Level 1 course.  Worked examples concentrate on fluorescence microscopy but the techniques used are widely applicable to other types of images.

- Lecture materials on GitHub (slides, worksheets and example data)

 

MATLAB for image processing

The course is formed of four 2-hour sessions, each introducing new concepts relevant to image processing and analysis:

- Session 1: Introduction to MATLAB, data types, conditional statements and loops
- Session 2: Matrix operations and image processing
- Session 3: Advanced data structures and object-oriented programming
- Session 4: Figures, plotting and user interfaces

Each session contains a PowerPoint presentation of new concepts and a practical exercise worksheet.  This workshop is suitable for anyone acquiring microscopy data as part of their research. No prior knowledge of MATLAB or programming is necessary or assumed.

- Lecture materials on GitHub (slides, worksheets and example data)

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