Microscopy

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)

An object detection function in ImageJ. [Analyze > Analyze Particles...]. It could simply be used for counting number of cells, but could also do more complex stuffs. ## Jython Snippet Here is a snippet of how to use Particle Analysis in Jython script.

In this workflow, you can use MorphoLibJ to generate accurate morphometric measurements

• First the fibers are segmented by mathematical morphology:
  • for example by using MorphoLibJ:
    • Create a marker image by creating a rough mask with extended regional maxima (similar to Find Max), such that you have one max per fiber
    • Use the marker controlled watershed (in MorpholLibJ/ Segmentation/ marker controlled watershed) : indicate the original grayscale image as the input, Marker will be your maxima image, select None for mask
    • it will create a label mask of your fibers
•  In MorphoLibJ /analyze/ select Region Morphometry: this will compute different shape factors which are more robust than the ones implemented by default in ImageJ
• Export the result table created to a csv file
• Then for example in Matlab or R, you can apply a PCA analysis (Principal component analysis) followed by a k-means with the number of class (clusters) (different fibers type) you want to separate.
• You can then add this class as a new feature to your csv file.
• From this you can sort your labelled fibers into these clusters for a visual feedback or further spatial analysis

This imageJ/Fiji plugin provides an analysis of the granulometry inside an image by mathematical morphology. It has sevral option for the structuring element to be used, and the size domain to be tested. The output will be both a curve of the remaining content of the image against the growing size of the structuring element, and the corresponding results table that could be then exported. It can deal with grayscale images directly, no need to segment the image first. This plugin can then be used to compare different texture based on some statistical analysis of the produced curve (for exemple comparison of the geometrical means to discriminate 2 textures). It is macro recordable as well. Programming Language: java Processes: successive erosion, dilation, closing or opening -> ANALYSIS User skills: Life Scientist, developers, analysts

MorphoLibJ is a library of plugin for ImageJ with functionalities for image processing such as filtering, reconstructing, segmenting, etc... Tools are based on Mathematical morphology with more rigorous mathematical approach than in the standard tools of ImageJ in particular for surface (or perimeter) measurements which are usually based on voxel counting.  

http://imagej.net/MorphoLibJ#Measurements

Among the features:

Morphological operations :  Dilation, Erosion, Opening,  Closing , Top hat (white and black), Morphological gradient (aka Beucher Gradient), Morphological Laplacian, Morphological reconstruction, Maxima/Minima , Extended Maxima/Minima -Watershed (classic or controlled) -Image overlay -Image labelling -Geodesic diameter -Region Adjacency Graph -Granulometry curves, morphological image analysis.