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

  • Go the Raw data tab:

    • Select the Location of the raw data by clicking on the icon and navigating to the folder where the tilt-series 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

    • 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 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

  • Click Save to save your settings

Step 2: Launch the 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

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

  • To inspect the streaming results, navigate to the Plots, Table, Gallery and Tilt Series 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 daemon track 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. Running seesions need to be canceled before they can be deleted

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

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

Filter tilt-series and export in star format

  • 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 resource parameters 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 .