A selection of teaching material on microscopy and bioimage analysis which I have compiled.

• Basics in Light Microscopy

  A once yearly theoretical and hands-on training for PhD and MSc candidates and core facility staff held at FCUL.

  First edition: October 2021

  Current edition: 2^nd

  Website of the last edition

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• High-throughput microscopy & screening

  Assorted ImageJ scripts.

  A seminar presented at the online workshop "Optical microscopy at COLife & Friends: learning the basics", from February 4, 2021.

• CellProfiler: Measuring organoid swelling in a time lapse experiment

  Tutorial: simple quantification of time-dependent organoid growth.

  Time lapse tracking practical exercise for the Neubias Training School 2 (Oeiras, 2017).

  https://github.com/hmbotelho/cellprofiler-practical2-NeuBIAS
• Time lapse analysis in CellProfiler, ImageJ and KNIME

  Tutorial: Analysis of time lapse microscopy data with CellProfiler, ImageJ and KNIME.

  SPAOM 2019 Community Workshop: Bioimage analysis open-source software tools. Contains Jupyter notebook.

  https://github.com/hmbotelho/SPAOM2019-ws2-bioimage-analysis-oss
• 2D and 3D high-content image analysis

  2D and 3D image analysis with CellProfiler.

  SPAOM 2020 Community Workshop: High-Content Screening.

  https://github.com/hmbotelho/SPAOM2020-ws1-high-content-screening
• Simple tutorial: image stitching and spatial calibration

  Stitching phase contrast microscopy images with the "collection/grid stitching" ImageJ plugin. Spatial calibration with a micrometric ruler.

  Plugin website. By Stephan Preibisch.