KLTPicker

KLT Picker: particle picking using data-driven optimal templates.

Current version: 1.2.8

Project's homepage: https://github.com/ShkolniskyLab/kltpicker

Date: 10/2020

This is the Python version containing the complete source code of the KLT Picker. A MATLAB version is available at https://github.com/ShkolniskyLab/kltpicker_matlab.

Please cite the following paper when using this package: Eldar A, Landa B, Shkolnisky Y. KLT picker: Particle picking using data-driven optimal templates. J Struct Biol. 2020 May;210(2) 107473.

Recommended Environments:

The package has been tested on Ubuntu 16.04 and Windows 10. It should probably work on other versions of Windows and Linux, but has not been tested on them yet. Similarly for macOS.

• Python 3.6.0+ is required.

• The package makes use of the pyfftw package, which in turn uses the FFTW library. Before installing KLTPicker make sure you have the FFTW library installed on your system: http://www.fftw.org/fftw3_doc/Installation-and-Customization.html#Installation-and-Customization

• For optional GPU support, the package requires:

  • NVIDIA CUDA GPU with the Compute Capability 3.0 or larger
  • CUDA Toolkit: v9.0 / v9.2 / v10.0 / v10.1 / v10.2 / v11.0

Install KLTPicker

Install KLTPicker via pip:

We recommend installing KLTPicker via pip:

$ pip install kltpicker

In order to enable the GPU support (provided that your system satisfies the above requirements):

$ pip install kltpicker[gpu]

Install KLTPicker from source

The tarball of the source tree is available via pip download kltpicker. You can install KLTPicker from the tarball:

$ pip install kltpicker-x.x.x.tar.gz

You can also install the development version of KLTPicker from a cloned Git repository:

$ git clone https://github.com/ShkolniskyLab/kltpicker.git

$ cd kltpicker

$ pip install .

Uninstall KLTPicker

Use pip to uninstall KLTPicker:

$ pip uninstall kltpicker

Upgrade KLTPicker

Just use pip with -U option:

$ pip install -U kltpicker

Getting started:

Please read the user manual for usage instructions, available at the homepage of the project on Github: https://github.com/ShkolniskyLab/kltpicker