ImageJ Macros

Evaluates the orientation of fiber orientation pattern and plots the results in the image. It calculates gradient in x and y direction. - then calculates the eigenvector of nematic tensor, which is the orientation of the pattern.

The workflow consists of firstly identifying spot (which can be also gravity center of cells identified by another method), and then secondly compute trajectories by linking these spots by global optimisation with a cost function. This method is part of the methods evaluated in Chanouard et al (2014) as "method 9" and is described in detail in its supplementary PDF (page 65).

Dependencies

Following plugins are required.

1. JAR to be placed under IJ plugin directory
2. A pdf file with instructions and output description is also available in the zip .
3. MTrackJ : Used for visualization of tracks. Preinstalled in Fiji.
4. Imagescience.jar: This library is used by MTrackJ. Use update site to install this plugin.
5. jama.jar. Preinstalled in Fiji.

##Advantages:

• support blinking (with a parameters allowing it or not)
• fast,
• can be used in batch, some analysis results provided.
• No dynamic model.
• The tracking part is not dependent of ImageJ.

Pitfalls:

• does not support division
• the optimization algorithm used is a simulated annealing, so results can be slightly different between two runs.
• No Dynamic model (so less good results but can be used for a first study of the kind of movements)

##The sample data

The parameters used for this example data Beads, were

1. detection: 150
2. the max distance in pixels: 20
3. max allowed disappearance in frame: 1

The root tools help to efficiently measure the following characteristics of plant roots: the angle of the opening of the whole root the depth to which it goes down the number of roots at multiple depths (for example 30cm, 35cm, ...) the diameters of the roots at multiple depths (for example 30cm, 35cm, ...)

Count bacterial colonies on agar plates and measure the occupied surfaces. The user has to provide a selection (roi) of the area that will be analyzed. He can than run the segmentation and if necessary correct the results. In a third step he can run the counting and measurement.

Normalize the orientation of the images of the Zebrafish embryos.

In the documentation webpage, the aim of the workflow is to normalize the orientation of the images of the Zebrafish embryos, find the point of injection of tumor cells and measure the distribution of Cy3 stained tumor foci.

ImageJ macro implementation of the Workflow described in Ghotra et al (2012). Note that currently only the angle and orientation normalization is implemented in this version.

Sample images are linked in the documentation webpage.