Links

A collection of links to useful or interesting resources

Image Analysis

Segmentation

  • Allen Cell Structure Segmenter
    Python-based open source toolkit for 3D segmentation of intracellular structures in fluorescence microscope images. Brings together classic image segmentation and iterative deep learning workflows. From Allen Institute.

  • cellpose: a generalist algorithm for cellular segmentation
    Python based. Online demonstration of segmentation of 2D images of cells. Drag and drop for segmentation of fluorescence, bright-field, and electron microscopy images. Animal and plant cells. Quite impressive. Code available on GitHub. Paper on ArXiv. From Janelia.

Online learning

Coding, tools

Deep Learning

  • Practical Deep Learning for Coders, v3
    Requires that you can code and have access to a GPU, but not much else. Uses Python and PyTorch, no Keras of TensorFlow here. Free and without adds, the way a good online course should be. From fast.ai (“Making neural nets uncool again”).

  • Deep Learning from the Foundations
    The second part of fast.ai’s course. Introduces Swift for TensorFlow. Focuses on foundations, as opposed to the practical aspects.