Ptolemy installation and setup¶

Automated square and hole finders are added to leginon to use Ptolemy (https://arxiv.org/abs/2112.01534) to determine optimal targets using computer vision algorithm and Convolutional Neural Network trained on user target selections accumulated at Simons Electron Microscopy Center at New York Biology Center (SEMC@NYSBC).

Not (Jan 2023): Ptolemy development has moved on without a release branch. If you want the version that is working and compatible with Leginon 3.6, Please checkout at the commit
SHA

f9105de58330bbb2abb4525a242be0e62340c59e

This implementation requires Ptolemy which has a separate license. For this release, the communication is through command line interface and rely on shared file system.

• At SEMC@NYSBC, Ptolemy, which was tested on python 3.9, runs in anaconda environment on the same CentOS7 computer where the main leginon process is.

Install Ptolemy and setup shell scripts to use its cli for grid square finding and exposure target hole finding¶