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

Microscopy

  • Basics in Light Microscopy

    Theoretical training course for undergraduate and researchers and core facility staff. Held at BioISI/FCUL.

    First edition: October 2021. I intend to make this a yearly training event. Course website.

  • 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.

Bioimage analysis

  • 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.