Python

The jicbioimage Python package makes it easy to explore microscopy data in a programmatic fashion (python).

Exploring images via coding means that the exploratory work becomes recorded and reproducible.

Furthermore, it makes it easier to convert the exploratory work into (semi) automated analysis work flows.

Features:

• Built in functionality for working with microscopy data
• Automatic generation of audit trails
• Python integration Works with Python 2.7, 3.3 and 3.4

The Huygens Remote Manager is an open-source, efficient, multi-user web-based interface to the Huygens software by Scientific Volume Imaging for parallel batch deconvolutions.

- 2D Stabilization in each slice of the stacks in time. - 3D Stabilization intravital imaging of all the stacks (including the dimension Z) - create the videos and the stabilized images in a new folder 2701

It is a tool to visualize and annotate volume image data of electron microscopy. Users can annotate objects (e.g. neurons) and skeleton structures. It provides the ability to overlaying the image data with user annotations, representing the spatial structure and the connectivity of labeled objects, and displaying a three dimensional model of it. It can be extended by plugins written in python. A similar, web-based implementation is being developed at webknossos.info. Example datasets are also available.