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

need a thumbnail

Fourier Bandpass Filter

Description

This is a plugin bundled with native ImageJ.

See IJ reference for more details > Link

need a thumbnail

Manual tracking with TrackMate

Description

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

has function

GIMP

Description

This is the official website of the GNU Image Manipulation Program (GIMP).

GIMP is a cross-platform image editor available for GNU/Linux, OS X, Windows and more operating systems. It is free software, you can change its source code and distribute your changes.

Whether you are a graphic designer, photographer, illustrator, or scientist, GIMP provides you with sophisticated tools to get your job done. You can further enhance your productivity with GIMP thanks to many customization options and 3rd party plugins.

CLI

example

gimp -i -b '(simple-unsharp-mask "foo.png" 5.0 0.5 0)' -b '(gimp-quit 0)'

More details, see here: GIMP Batch Mode

Log3D

Description

The freely available software module below is a 3D LoG filter. It applies a LoG (Laplacian of Gaussian or Mexican Hat) filter to a 2D image or to 3D volume. Here, we have a fast implementation. It is a perfect tool to enhance spots, like spherical particles, in noisy images. This module is easy to tune, only by selecting the standard deviations in X, Y and Z directions.

IJ Macro command example

run("LoG 3D", "sigmax=1 sigmay=1 sigmaz=13 displaykernel=0 volume=1");

ImagePy

Description

This note presents the design of a scalable software package named ImagePy for analysing biological images. Our contribution is concentrated on facilitating extensibility and interoperability of the software through decoupling the data model from the user interface. Especially with assistance from the Python ecosystem, this software framework makes modern computer algorithms easier to be applied in bioimage analysis.

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.

has function

DEFCoN-ImageJ

Description

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

has topic

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

has function

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.