Leginon

h1. 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.

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.

h2. Install Ptolemy and setup shell scripts to use its cli for [[Setup Ptolemy CLI shell script|grid square finding]] and [[Setup Ptolemy CLI for exposure targeting|exposure target hole finding]]

h2. Upload MSI-Ptolemy application into leginon database

Follow the instruction in [[Applications|web application tools]]

* Note: If your system needs two Leginon client opened, each on a different pc, use MSi-Ptolemy2.xml

If you have your own application you can do the following replacement by [[Use_the_Application_Editor_to_create_Leginon_applications|editing your application]] :

Square Targeting Node : MosaicClickTargetFinder class => MosaicScoreTargetFinder

Exposure Targeting Node: JAHCFinder => ScoreTargetFinder