Automated Data Collection

Load a sample file and SERGUI collects your samples for you. For every sample you mark, it mounts the sample, aligns the loop, runs a 3D raster, screens and indexes, sets exposure and transmission, collects the data set and processes it.

Automation at Upgraded SER-CAT (PDF)

How long it takes

  • Screening: about 1 minute per sample
  • Data collection: about 2–3 minutes per sample with the default parameters
  • A full puck (16 samples): about 50 minutes. By hand, users typically manage about 10 samples per hour.

1. Prepare your sample file

  • Template: in SERGUI, choose Document → Download SER-CAT Sample Template File. It saves sercat-sample.xlsx in your main data directory. Edit it and load it back into SERGUI.
  • File type: an Excel .xlsx file.
  • Columns: the file needs five columns labelled Puck, Pin, Sample, Resolution, AutoCollect. You can add extra columns for your own notes.
  • Puck: names must match the pucks loaded in SERGUI (the Puck list). If they don't, ask staff to rename the loaded pucks, or edit your file and reload it.
  • Names: Puck and Sample names can't contain spaces or special characters. Only - and _ are allowed.
  • Pin: a number from 1 to 16.
  • AutoCollect: any entry marks the sample for collection. Leave the cell empty to skip that sample.

2. Set up on the Automation tab

  • Load Sample File: loads your .xlsx file.
  • Edit Sample File: opens your loaded file for editing. Save it and close the editor, and SERGUI reloads it automatically.
  • Edit Collect Parameters: sets Scan Width, Exposure Time, Transmission and Degree Range for all samples.
    • Resolution left empty: screening uses 200 mm (1.5 Å), and data collection uses each sample's Resolution from your file.
    • Resolution entered: your value overrides the file for all screening and collection.

3. Run automation

  • Option 1 – Screen Sample Only: screens every sample in the file (mount → loop centering → 2D raster → single image → autoindex). Check the results with View Screen Log.
  • Option 2 – Collect Data Sets: collects only the samples marked in AutoCollect (mount → loop centering → 3D raster → screen → data set → autoprocess). Check the results with View Data Log.

Important: don't use SERGUI while automation is running. The screen shows progress, and SERGUI becomes usable again when automation finishes.