First-time autoscreening setup » History » Version 3
Anchi Cheng, 03/01/2022 12:45 AM
1 | 1 | Anchi Cheng | h1. Smart-leginon multi-grid autoscreening |
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3 | 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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5 | 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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7 | * 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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9 | 3 | Anchi Cheng | h2. Install Ptolemy and [[Setup Ptolemy CLI shell script|setup shell script to use its cli]] |
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11 | 2 | Anchi Cheng | h2. Square finding localization and classification using MosaicExternalScoreFinder |
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13 | 2 | Anchi Cheng | (node alias Square Finding) |
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15 | h3. Upload MSI-Ptolemy application into leginon database |
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17 | Follow the instruction in [[Applications|web application tools]] |
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18 | * Note: If your system needs two Leginon client opened, each on a different pc, use MSi-Ptolemy2.xml |
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20 | If you have your own application you can do the following replacement by [[Use_the_Application_Editor_to_create_Leginon_applications|editing your application]] : |
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22 | Square Targeting Node : MosaicClickTargetFinder class => MosaicScoreTargetFinder |
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23 | Exposure Targeting Node: JAHCFinder => ScoreTargetFinder |
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25 | h3. Define target area size sampling in Leginon |
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27 | Do this in the settings next to "acquisition" target panel. Enter |
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29 | # Maximal number of squares to select |
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30 | # Number of target group to sample |
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32 | For example, total of 12 squares selected in 3 groups means the program divided out all blob squares with valid area range into 3 size group (small, medium,and large). It then choose 4 blob squares in each group with highest score given by Ptolemy as the output square targets. High score in Ptolemy result means it is more likely to be a good square. |
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34 | 3 | Anchi Cheng | h3. Set the limits of square area range |
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36 | This is set in "Thresholded" settings. However, it is easier to set by select examples once you acquire your first grid atlas in this node. |
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38 | h3. |