Free and open source

An ImageJ plugin for selecting a plane in focus among multiple slices image stack. The algorithm uses normalized variance. A short tutorial is available in the plugin web page (above).

The tool measures the total length of the microtubules in a 3D image.

See: http://dev.mri.cnrs.fr/projects/imagej-macros/wiki/Microtubules_Tool_(3…

You can find a test image here.

The Arabidopsis Seedlings Tool allows to analyze the germination and seedling growth of Arabidopsis (Arabidopsis thaliana) in liquid culture. It measures the surface of green pixels per well in images containing multiple wells. It can be run in batch mode on a series of images. It writes a spreadsheet file with the measured area per well and saves a control image showing the green surface that has been detected per well. 

See http://dev.mri.cnrs.fr/projects/imagej-macros/wiki/Arabidopsis_Seedlings_Tool

Test images can be found here.

**Python(x,y)** is a free scientific and engineering development software for numerical computations, data analysis and data visualization based on Python programming language, Qt graphical user interfaces and Spyder interactive scientific development environment. Many python libraries related to numerical calculation are packaged, so you do not need to search and install them individually. Included libraries are listed **[here](https://code.google.com/p/pythonxy/wiki/StandardPlugins).**