Image analysis workshop

Participants will learn the fundamentals of microscopy image analysis using ImageJ/Fiji.

Target audience:
 - beginners in image analysis
 - people with a few years of image analysis experience

Learning objectives

• Understand image bit depth, file formats and metadata
• Working with multi-dimensional images (channels, time series)
• Perform common image processing tasks in Fiji more effectively:
  • adjusting brightness/contrast
  • Adding scale bar
  • ROIs
  • Intensity measurements
• Understand when to use image processing filters (Gaussian, Edge detection etc.) to help with cell/nucleus segmentation.

Prerequisite

Participants are recommended to bring their own laptops with the latest Fiji installed.

Opening images, Image file formats, bit-depth, metadata

drag and drop - TIFF, PNG
Bio-Formats for others
Opening large images with different resolutions
Bio-Formats - crop on import

bit-depth

dynamic range - https://svi.nl/DynamicRange

converting between bit depths - scale when converting (image clipping https://svi.nl/Image-Clipping)

Working with multidimensional images (Channels, time series)

Brightness/Contrast, Histogram

Scale bar

Thresholding - binary and label images

ROIs, overlays

Intensity measurements

Image processing filters and Deep Learning

• Gaussian
• Edge detection (Canny)