Contents

Tomography session

Tomography session

This tutorial shows how to process tilt-series on-the-fly during data collection. nextPYP implements streaming using two parallel tracks:

  • File transfer from the microscope computer to a permanent storage location

  • Data pre-processing consisting of frame alignment, tilt-series alignment, CTF estimation, tomogram reconstruction and particle picking

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

  • From the Dashboard, click on Go to Sessions

  • Start a Tomography session using + Start Tomography

  • Give the session a Name and assign a Group from the dropdown menu (see Administration to create and assign users to groups)

  • Go the Raw data tab:

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

    • Click on the Gain reference tab

    • Specify the path and parameters for the gain reference

    • Click on the Microscope parameters tab

    • Specify Pixel size (A), Acceleration voltage (kV), and the approximate Tilt-axis angle (degrees)

    • Click on the Session settings tab

    • Set Number of tilts to the number of tilts in each tilt-series. This parameter tells nextPYP when a tilt-series is complete and ready to be processed

    • Click on the Frame alignment tab

    • Select Single-file tilt-series if acquiring tilt-series as a single file. Otherwise, provide the Frame pattern to let nextPYP know what files to look for

    • Click on the Resources tab

    • Select the number of Threads per task, Memory per task, and other relevant parameters (see Computing resources)

  • Click Save to 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 daemon at any time using the Cancel button

  • To inspect the streaming results, navigate to the Plots, Table, Gallery and Tilt Series 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

Delete or Start a session using settings from an existing session

  • You can delete a session by clicking on the icon . This will delete the session and all files produced during pre-processing

  • You can create a new session with the same settings as an existing session using the icon

Step 5 (optional): Filter tilt-series and export metadata

Filter tilt-series and export to external programs in star format

  • You can filter tilt-series according to different criteria in 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 resources to run the export job. After clicking 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 .

See also

previous

Single-particle session

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Import/export projects