elsword016 / swc-plugins-for-imaris-10 Goto Github PK

Based on the original implementation by Sarun Gulyanon (2018). Re-implemented from scratch for Imaris 10.0.1 and Python 3.7 and updated some things like generation and saving individual filaments separately and exports more consistent with the .swc specifications.

Used for additional analysis of the paper:

Automated neuronal reconstruction with super-multicolour fluorescence imaging

Marcus N. Leiwe, Satoshi Fujimoto, Toshikazu Baba, Daichi Moriyasu, Biswanath Saha, Richi Sakaguchi, Shigenori Inagaki, Takeshi Imai [bioRxiv 2022] [github]

Based on the Breadth-first search (BFS) - algorithm for searching a tree data structure for a node that satisfies a given property. It starts at the tree root and explores all nodes at the present depth before moving on to the nodes at the next depth level.

• ImarisXT license
• Imarisbridge
• ImarisLib
• Python 3.7

1. ExportSWC_new.py- Export any Imaris filaments as swc morphology- separate and in a single combined file.
2. ImportSWC_new.py - Import any swc morphology as Imaris filaments.

Standard .swc morphologies only (no swc+).

Data imported/exported follows the Neuromorpho specifications should look like this:

• Encoding: ASCII text
• Limitations: no markers, no spines.
• Comment lines begin with character '#'.
• Subsequent non-empty lines each represent a single neuron sample point with seven data items.

Place in the folder with the ImarisLib library folders (default is C:/ProgramFiles/Bitplane/Imaris10/XT/python3/) and then run it from the Imaris window and follow the prompts on the GUI.