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Ptolemy installation and setup » History » Version 3

Anchi Cheng, 01/05/2023 11:33 AM

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h1. Ptolemy installation and setup
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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).
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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
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SHA 
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f9105de58330bbb2abb4525a242be0e62340c59e
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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.
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* 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.
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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]]