Detection of Molecules - DoM

Description

A collection of components for super resolution image data:

  • Detect Molecules
  • Reconstruct Image
  • Results table
  • Drift correction
  • Chromatic correction

Temporal Medial Filter

Description

This component can be used to find moving foreground features, which can be a powerful way to suppress false background detections in subsequent tracking steps.

set time window, and standard deviations above background for foreground time window should be more than 2x larger than time taken for a feature to traverse a pixel (NB. total window is 2x half-width +1) moving foreground identified by intensity increase relative to background average (i.e. median) for a pixel over a given time window "soft" segmentation, yielding foreground probability related to excess intensity (in standard deviations) over background level crude Anscombe transform applied to data to stabilize the variance

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Fourier Bandpass Filter

Description

This is a plugin bundled with native ImageJ.

See IJ reference for more details > Link

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Manual tracking with TrackMate

Description

Manual tracking using Trackmate plugin (comes with FIji, so no installation required if you are using Fiji). 

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Jama

Description

JAMA is a basic linear algebra package for Java. It provides user-level classes for constructing and manipulating real, dense matrices. It is meant to provide sufficient functionality for routine problems, packaged in a way that is natural and understandable to non-experts. It is intended to serve as the standard matrix class for Java, and will be proposed as such to the Java Grande Forum and then to Sun. A straightforward public-domain reference implementation has been developed by the MathWorks and NIST as a strawman for such a class. We are releasing this version in order to obtain public comment. There is no guarantee that future versions of JAMA will be compatible with this one.

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PHANTAST for FIJI

Description

 

The phase contrast microscopy segmentation toolbox (PHANTAST) is a collection of open-source algorithms and tools for the processing of phase contrast microscopy (PCM) images. It was developed at University College London's department of Biochemical Engineering and CoMPLEX.

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DEFCoN-ImageJ

Description

An ImageJ plugin for DEFCoN, the fluorescence spot counter based on fully convolutional neural networks

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Align slices in stack

Description

Align_slices in stack utilized the template matching function cvMatch_Template to do slice registration(alignment) based on a selected landmark.
This function will try to find the landmark or the most similar image pattern in every slice and translate each slice so that the landmark pattern will be the same position throughout the whole stack. It could be used to fix the drift of a time-lapse image stacks.

Source code: link

Input data: image stack
output data: image stack

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cvMatch_Template

Description

It implements the template matching function from the OpenCV library. The java interface of OpenCV was done through the javacv library. It is quite similar as the existing template matching plugin but runs much faster and users could choose among six matching methods: 

1.Squared difference

2.Normalized squared difference

3.Cross-correlation

4.Normalized cross-correlation

5.Correlation coefficient

6.Normalized correlation coefficient

The detailed algorithms could be found here.

The cvMatch_Template will search a specific object (image pattern) over an image of interest by the user-specified method. 

Template Matching and Slice Alignment--- ImageJ Plugins

Description

This ImageJ plugin contains two functions. The first one is the cvMatch_Template. It implements the template matching function from the OpenCV library. The second function Align_slices in stack utilized the previous matching function to do slice registration(alignment) based on a selected landmark. 

For more details, refer to the page of each component. 

cvMatch_Template

Align Slices in Stack

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