Lab Links

• Skala Lab Github Repository - Code repository for the lab (private)
• DoIT Software Library - Link to software provided by the university

Hardware Control

• MicroManager - open source microscope control

Segmentation and Particle Tracking

• Allen Cell Structure Segmenter - Python-based open source toolkit for 3D segmentation of intracellular structures in fluorescence microscope images.
• Imagej - Java image processing program inspired by NIH Image
• ImageJ2 - Update to ImageJ
• Mosaic Suite (Imagej plugin) - Several of the image-processing algorithms developed at the MOSAIC Group ( 2D/3D single-particle tracking)
• Icy - An open community platform for bioimage informatics
  • Kelsey
• CellProfiler - Cell image analysis software
• TrackMate(ImageJ Plugin) - particle tracking analysis tool

Machine Learning

• MitoMo - Automated image/video processing software for mitochondria
  • Amani
• maskrcnn - an implementation of Mask R-CNN on Python 3, Keras, and TensorFlow
  • Christine
• CSBDeep - a toolbox for content-aware restoration of fluorescence microscopy images (CARE), based on deep learning via Keras and TensorFlow.
  • Christine

Programming

• Python
  • Anaconda Distribution - open-source Anaconda Distribution is the easiest way to perform Python/R data science and machine learning
  • Spyder IDE (Also comes with Anaconda)
    • Emmanuel
  • PyCharm IDE
    • Emmanuel
• MATLAB
• R

Libraries

• Bioformats - software tool for reading and writing image data using standardized, open formats

Other tools relevant but not yet explored

• SuperSegger - Segment, visualize and analyze your data. Optimized for rod-like bacteria cells
• Oufti - software package designed for analysis of microscopy data
• Morpheus - software package for morphometric analysis
• ilastik - tool for interactive image classification, segmentation and analysis
  • 1)Pixel Classification Tutorial
  • 2)Object Classification
  • Playlist of Tutorials
• OMERO - secure central repository for storing images

Other

• Theme Documentation