Single-particle session
Contents
Single-particle session¶
This tutorial shows how to process micrographs on-the-fly during data collection. nextPYP implements streaming using three parallel tracks:
File transfer from the microscope computer to a permanent storage location
Data pre-processing consisting of frame alignment, CTF estimation and particle picking
2D classification to monitor particle quality
Each track is displayed in a separate row and has its own Status indicator and Controls to Start, Restart, Clear, or Stop the session and to display the Logs
Step 1: Create a new session¶
Streaming is organized in sessions. A new session should be created for each data collection run
Go to the Dashboard and click on Go to Sessions
Start a Single-particle session by clicking on + Start Single-particle
Give the session a Name and assign a Group from the dropdown menu (see Administration to create and manage user groups)
Go to the Image data tab:
Select the
Locationof the raw data by clicking on the icon and navigating to the folder where the movies are savedClick on the Gain reference tab
Specify the location and parameters for the gain reference as needed
Click on the Microscope parameters tab
Set the
Pixel size (A)andAcceleration voltage (kV)Click on the Particle detection tab
Set the
Particle radius (A)Click on the Resources tab
Set the number of
Threads per task,Memory per task, and other resources as needed (see Computing resources)
Save your settings
Step 2: Launch the streaming session¶
Start data pre-processing
Go to the Operation tab and Start the daemon from the Controls panel
You may stop the session at any time using the Cancel button
Inspect the results by navigating to the Plots, Table, Gallery, Micrographs, and 2D Classes tabs
Step 3 (optional): Adjust data processing parameters¶
Change data processing parameters during a session
You can change the data processing settings during a session by going to the Settings tab and saving your changes
Restart the corresponding daemon tracks for the changes to take effect
Step 4: Copy or delete a session¶
Start a session using settings from an existing session or delete a session
You can create a new session by copying the settings of an existing one by clicking on the icon
You can delete a session by clicking on the icon . This will permanently delete the session and all associated files
Step 5 (optional): Filter micrographs and export metadata¶
Filter micrographs and export to external programs in star format
You can filter micrographs according to different criteria by going to the Table tab. Type a filter name and click Save. Add and apply filters as needed and click Save when you are done
Click Export to export the data in
starformat. A dialog will appear where you can specify the resources for the export job. After clicking on Export a new job will appear in the Operation tab and you will be able to check its status and see the location of the exported data by clicking on the icon .