TomoBlob

Blob-like particle detection and picking 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

TomoBlob is a software package that facilitates automated detection of blob-like features in electron (cryo-)tomograms. It consists of two programs to be applied in sequence. The first program, blobs3d, processes the input tomogram and detects blobs. Two methods for blob detection are implemented, the Laplacian of Gaussian (LoG) and the Determinant of Hessian (DoH). The second program, blobs3dpick, extracts the coordinates of the blobs and writes them on a text file. The package accepts tomograms in MRC format and writes the coordinates in formats compatible with IMOD and Relion.

If you use TomoBlob 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: tomoblob.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 TomoBlob has been supported by the Fundacion Ramon Areces. Additional funds were obtained from the Spanish AEI and Huntington's Disease Society of America.