NeuroR

NeuroR is a collection of tools to repair morphologies. There are presently three types of repair which are outlined below.

Sanitization

This is the process of sanitizing a morphological file. It currently:

• ensures it can be loaded with MorphIO
• raises if the morphology has no soma or of invalid format
• removes unifurcations
• set negative diameters to zero
• raises if the morphology has a neurite whose type changes along the way
• removes segments with near zero lengths (shorter than 1e-4) Note: more functionality may be added in the future

Cut plane repair

The cut plane repair aims at regrowing part of a morphologies that have been cut out when the cell has been experimentally sliced. neuror cut-plane repair contains the collection of CLIs to perform this repair. Additionally, there are CLIs for the cut plane detection and writing detected cut planes to JSON files:

• If the cut plane is aligned with one of the X, Y or Z axes, the cut plane detection can be done automatically with the CLIs:

• If the cut plane is not one the X, Y or Z axes, the detection has to be performed through the helper web application that can be launched with the following CLI:

Unravelling

Unravelling is the action of “stretching” the cell that has been shrunk because of the dehydratation caused by the slicing. The unravelling CLI sub-group is:

The unravelling algorithm can be described as follows:

• Segments are unravelled iteratively.

• Each segment direction is replaced by the averaged direction in a sliding window around this segment.

• The original segment length is preserved.

• The start position of the new segment is the end of the latest unravelled segment.