Installation

Installing bombcell

To begin using Bombcell:

• clone the repository and the dependencies.
• add bombcell's and the dependancies' folders to MATLAB's path.
• in addition, if you want to compute ephys properties, change your working directory to bombcell\+bc\+ep\+helpers in matlab and run mex -O CCGHeart.c to able to compute fast ACGs, using part of the FMAToolbox.

Dependencies

• npy-matlab, to load .npy data in.
• If you have z-lib compressed ephys data, compressed with mtscomp, you will need the zmat toolbox. More information about compressing ephys data here.
• prettify-matlab, to make plots pretty.
• MATLAB toolboxes:
  • Signal Processing Toolbox
  • Image Processing Toolbox
  • Statistics and Machine Learning Toolbox
  • Parallel Computing Toolbox
  • Optimization Toolbox

In addition we would like to acknowledge:

• to compute fast ACGs, we use a function (CCGHeart.c) part of the FMAToolbox, and it is already included in bombcell.
• to read in spikeGLX meta data, we use a function from Jennifer Colonell's SpikeGLX_Datafile_Tools repository.

Requirements

MATLAB

Bombcell requires MATLAB >= 2019a. In previous version, the built-in function parquetwrite that bombcell uses does not exist.

Operating system

Bombcell has been successfully used on Ubuntu (20.04 LTS "Focal Fossa"), Debian (11 "Bullseye" and 12 "Bookworm") and Windows 9, 10 and 11.

Recording probes

Bombcell has been tested with Neuropixels (3A, 1.0, 2.0). It might need a few changes to properly work for other probes. In that case, please create a github issue or email us and we will implement them for you!

Recording software

Bombcell has been tested with SpikeGLX and OpenEphys. It might need a few changes to properly work for other software. In that case, please create a github issue or email us and we will implement them for you!

Spike-sorter

Bombcell has been tested with Kilsort. It will need changes to properly work for other spike-sorters. In that case, please create a github issue or email us and we will implement them for you!