Manual tracking with TrackMate

Description

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

has function

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");

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. 

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

has function

CSBDeep, a toolbox for Content-aware Image Restoration (CARE) in Knime

Description

Deep learning based restoration, with guidelines for training. See also the Fiji plugin.

CSBDeep, a toolbox for Content-aware Image Restoration (CARE) in Fiji

Description

Deep learning for fluorescence image restoration (denoising, deconvolution). Requires training on your data set but the procedure is described.

CARE

HyphaTracker

Description
HyphaTrackerWorkflow
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.

hyphatracker