Blogs and article series
- Jake VanderPlas's excellent blog on using Python for data analysis
- John Kruschke's blog, Doing Bayesian Data Analyis
- Points of View series from Nature Methods on visualization of biological data
- Points of Significance series from Nature Methods on good statistical practices
Online tutorials
- Caltech BE/Bi/NB 203: Introduction to Programming Bootcamp, a set of tutorials and exercises to learn basic Python programming for scientific applications
- Zed Shaw's Learning Python the Hard Way, a good way to learn basic Python
- Code Academy Python tutorial, another good resource for learning Python
- 10 minutes to pandas
- Lectures on scientific python (a couple especially good ones have links below)
- Segmentation using scikit-image
- SciPy lecture on basic image processing
- More advanced SciPy lecture on image processing
- Dan White's excellent intro to image processing
- Collection of teaching materials from the Biopolis Dresden Imaging Platform
Useful Python tools
- Anaconda: scientific Python distribution with conda package manager
- Enthought Canopy: scientific Python distribution
- Jupyter: web app for interactive computing (with documentation)
- IPython: interactive Python
- NumPy: numerical methods with Python
- SciPy: suite of scientific software
- matplotlib: plotting utilities
- pandas: data handling utilities
- scikit-image: image processing toolkit
- seaborn: beautiful statistical plotting software the uses statsmodels to do calculations under the hood.
- pybeeswarm: plotting utility
- emcee: Markov chain Monte Carlo with a simple interface
- scikit-learn: machine learning
- numdifftools: numerical differentiation tool
- statsmodels: statistical analysis software
- pymc3: Markov chain Monte Carlo
- pystan: Python wrapper around STAN MCMC package
- mahotas: biological-minding image processing toolkit
- PyWavelets: Package for doing wavelet calculations
- mayavi: 3D visualization
- Bokeh: beautiful graphics
- Awesome Python: a list of useful packages
Other image processing tools
- ImageJ: NIH-sponsored biological image processing suite
- ImageJ2: an in-progress re-write of ImageJ
- Fiji: ImageJ, batteries included!
- ilastik: an interactive learning and segmentation toolkit
- Insight Segementation and Registration Toolkit (ITK): sophisticated system for segmentation
- CellProfiler: Java-based cell segmenter
- Icy: platform for bioimage informatics
- OpenCV: computer vision software
- LOCI Bio-Formats: tools to convert between image formats
Miscellaneous
- ColorBrewer2: colormap generator