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 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). Optional: change the default folder where the data for the session will be saved

  • Go to the Raw data tab:

    • Select the Location of the raw data by clicking on the icon and navigating to the folder where the movies are saved

    • Click 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) and Acceleration voltage (kV)

    • Click on the Session settings tab

    • Select a Raw data transfer method between “move”, “copy”, or “link”. Warning: “move” will copy the raw data to the session folder and delete it from the original location!

    • Click on the Particle detection tab

    • Set the Particle radius (A)

    • Select “auto” or “all” as the Method

    • Click on the Resources tab

  • Save your settings

Step 2: Launch the session

Start data pre-processing

  • Go to the Operation tab and click Start in the Controls panel. This will also start the Data pre-processing and 2D classification daemons

  • You may stop the session at any time using the Cancel button

  • Monitor storage utilization, data transfer progress, and speed in the Operation tab

  • Inspect the streaming results by navigating to the Plots, Table, Gallery, Micrographs, and 2D Classes tabs

Step 3 (optional): Change 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, adjusting parameters as needed, and saving your changes

  • Restart the Data pre-processing and/or the 2D classification 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. Running seesions need to be canceled before they can be deleted

Step 5 (optional): Filter and export micrographs

Filter micrographs and export in star format

  • 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 star format. A dialog will appear where you can specify the resource parameters 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 .