Introduction to Bioimage analysis

Introduction to Bioimage analysis (a soft introduction to)

Rocco D’Antuono
Crick Advanced Light Microscopy STP, The Francis Crick Institute (London, UK)

This section is divided in 3 parts:

• Introduction to Bioimage analysis

• It’s time to play! Exercises on visualization, inspection, and image segmentation using common image analysis software (napari, FIJI, CellProfiler)

• Inspire the developers! wanted software functionalities

Slides: https://drive.google.com/file/d/1BNkMPtYxnyANF1srXI6B6P-J_torzDiS/view?usp=sharing

Repository: RoccoDAnt/Basic-digital-imaging_protocols

Image Data:

• 3D image data - High-Resolution Episcopic Microscopy (HREM - Mouse Embryo)

• Wide-field fluorescence images of stained cell nuclei, cytoplasms, vesicles

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Some exercises

Image inspection
Fig. 4.7 of D’Antuono, R. (2022). Basic Digital Image Acquisition, Design, Processing, Analysis, Management, and Presentation. In: Nechyporuk-Zloy, V. (eds) Principles of Light Microscopy: From Basic to Advanced . Springer, Cham. https://doi.org/10.1007/978-3-031-04477-9_4

3D rendering in napari
Fig. 4.9 of D’Antuono, R. (2022). Basic Digital Image Acquisition, Design, Processing, Analysis, Management, and Presentation. In: Nechyporuk-Zloy, V. (eds) Principles of Light Microscopy: From Basic to Advanced . Springer, Cham. https://doi.org/10.1007/978-3-031-04477-9_4

Count and measure cells with python
Fig. 4.11 of D’Antuono, R. (2022). Basic Digital Image Acquisition, Design, Processing, Analysis, Management, and Presentation. In: Nechyporuk-Zloy, V. (eds) Principles of Light Microscopy: From Basic to Advanced . Springer, Cham. https://doi.org/10.1007/978-3-031-04477-9_4