General image analysis

Microscope autopilot


AutoPilot is the open source project that hosts the general algorithm for fast and robust assessment of local image quality, an automated computational method for image-based mapping of the three-dimensional light-sheet geometry inside a fluorescently labeled biological specimen, and a general algorithm for data-driven optimization of the system state of light-sheet microscopes capable of multi-color imaging with multiple illumination and detection arms.

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Find Maxima (Python)



Maxima finding algorithm recreated from implementation in Fiji(ImageJ)

This is a re-implementation of the java plugin written by Michael Schmid and Wayne Rasband for ImageJ. The original java code source can be found in: 

This implementation remains faithful to the original implementation but is not 100% optimised. The java version is faster but this could be alleviated by compiling c code for parts of the code. This script is simply to provide the functionality of the ImageJ find maxima algorithm to individuals writing pure python script.

find maxima comparison.

2D Gaussian fitting macro (Fiji/ImageJ) for multiple signals.


This script includes a rough feature detection and then fine 2D Gaussian algorithm to fit Gaussians within detected regions. This macro is unique because the ImageJ/Fiji curve fitting API only supports 1-D curve. I get around this by linearising the equation. This implementation is for isotropic (spherical) or anistropic (longer in x/y) diagonally covariant Gaussians but not fully covariant Gaussians (anisotropic and rotated). 



Bisque (Bio-Image Semantic Query User Environment) : Store, visualize, organize and analyze images in the cloud. It also allow to run workflows using a set of deployed tools, such as CellProfiler, RootTipMultin Nuclear Tracker, Microtubule tracker etc...

Bisque was developed for the exchange and exploration of biological images.

The Bisque system supports several areas useful for imaging researchers from image capture to image analsysis and querying. The bisque system is centered around a database of images and metadata. Search and comparison of datasets by image data and content is supported. Novel semantic analyses are integrated into the system allowing high level semantic queries and comparison of image content.

  • Bisque is free and open-source
  • Flexible textual and graphical annotations
  • Cloud scalability: PBs of images, millions of annotations
  • Distributed storage: local, iRODS, S3
  • Integrated image analysis, high-throughput with Condor
  • Analysis in MATLAB, Python, Java+ImageJ
  • 100+ biological image formats
  • Very large 5D images (100+ GB)
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bisque screenshot

Galaxy Image Analysis Tools


Image analysis tools to be used within Galaxy

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Galaxy imaging workflow


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HyphaTracker Workflow

HyphaTracker propose a workflow for time-resolved analysis of conidia germination. Each part of this workflow can also be used independnatly , as a toolbox. It has been tested on bright-field microscopic images of conidial germination. Its purpose is mainly to identify the germlings and to remove crossing hyphae, and measure the dynamics of their growth.


kymograph generation


Kymograph generation under ImageJ:

one simple solution, plot a line (ROI line) on the first frame, where you want to generate the kymograph.


Image  / Stacks  / Reslice

It will generate a new image were Y dimension is the time, and X the position on the line you have drawn.

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A software toolkit for computational morphometry of biomedical images, CMTK comprises a set of command line tools and a back-end general-purpose library for processing and I/O.

The command line tools primarily provide the following functionality: registration (affine and nonrigid; single and multi-channel; pairwise and groupwise), image correction (MR bias field estimation; interleaved image artifact correction; EPI unwarping), processing (filters; combination of segmentations via voting and STAPLE; shape-based averaging), statistics (t-tests; general linear model).

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Globals for Images SimFCS 4


Software for analysis, visualization, simulation, and acquisition  of data from spectroscopy and fluorescence microscopy.

  • Fluorescence Correlation Spectroscopy (FCS)
  • Fluorescence Lifetime Imaging (FLIM) and Phasor plots
  • Förster Resonance Energy Transfer (FRET)
  • Generalized Polarization (GP) and Spectral Phasors
  • Number and Brightness (N&B)
  • Photon Counting Histogram (PCH)
  • Raster and Spatio-temporal Image Correlation Spectroscopy (RICS and STICS)
  • Single Particle and Modulation Tracking (SPT, MT)
  • Image Mean Square Displacement (iMSD)
  • Pair correlation function (pCF)
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Measures wound-healing assay videos, 

 For each video, the velocity and the order parameter are analyzed in time and space to extract quantitative parameters characterizing the cell motility phenotype. The different conditions (videos) can then be classified according to these parameters.