TomoSpatStat

Spatial and Neighbour Analysis in (cryo-)ET

E. Martin-Solana (1), M.R. Fernandez-Fernandez (2,3), J.J. Fernandez (2,3),

(1) University of Pittsburgh. Pittsburgh. USA.

(2) Spanish National Research Council (CINN-CSIC). Oviedo. Spain.

(3) Health Research Institute of Asturias (ISPA. Oviedo. Spain.

Contact: jjfernandez.software @ gmail.com

Description

TomoSpatStat is a software package that facilitates the statistical analysis of the 3D spatial distribution of structures in a tomogram. It includes second-order spatial point pattern analysis with the Ripley's K function, which measures the expected number of ocurrences within a distance from an arbitrary ocurrence of the target structure, normalized by the density of the distribution. Additionally, the program can also perform n-order Nearest Neighbour analysis by estimating the distribution of distances from an arbitrary ocurrence of the target structure to their n nearest neighbours. The program tomospatstat requires an input text file with the coordinates of the structures in a tomogram and writes the results of the analysis in a text or CSV file for subsequent plotting and/or further analysis with statistical tools.

If you use TomoSpatStat in your works, please cite the following article:

Progressive alterations in polysomal architecture and activation of ribosome stalling relief factors in a mouse model of Huntington's Disease.

Martin-Solana et al.

Neurobiology of Disease 195:106488, 2024.

https://doi.org/10.1016/j.nbd.2024.106488

Download the package

Current version: 1.0 (April 2024)

Available material:

Documentation in PDF: tomospatstat.pdf
Binaries for x86-based platforms under Linux (64 bits) and Windows WSL.
Binaries for Macs based on Intel and Apple Silicon processors under OSX/macOS.

The development of TomoSpatStat has been supported by the Fundacion Ramon Areces. Additional funds were obtained from the Spanish AEI and Huntington's Disease Society of America.