Calibration of direct laser writing systems

Note: If you want to use this procedure, first check the scribe-calibration-data repository to see if someone else has already measured calibration data for your system. If so, you can download the calibration_data folder and index.txt file, placing them in the top directory of this repository. This will allow you to skip steps 1-6, which are fairly time consuming (~20 hours).

Calibration Procedure:

1. Fabricate calibration devices.

2. Measure calibration devices.

3. Calculate calibration curves.

4. Fabricate prisms.

5. Measure prisms.

6. Calculate refractive index function.

   After this initial procedure, the necessary data for calibration has been computed, and designs for optical elements may be calibrated and fabricated.

   Operating Procedure:

7. Design a refractive index profile, analogous to those in the example_devices folder. This profile can either be 2D (and specify the thickness) or be 3D.

8. Use the helper function in calibration_utility.py to convert the refractive index profile to a fluorescence intensity target profile.

9. Store the resulting intensity profile in a Device (defined in device_data.py) and save it as a pickled file in the device_input directory.

10. Check/modify the settings in calibration_settings.py.

11. Run run_calibrate_device.py. By default, it will multithread and use the maximum number of cores to generate the calibrated files as fast as possible.

12. Copy the GWL files from device_input to source_gwl/device.

13. Check/modify the settings at the top of assemble_master_file.py.

14. Run assemble_master_file.py.

15. Copy the entire source_gwl directory to the cloud or a USB drive. Copy it onto the Nanoscribe computer, and load MasterFile.gwl as the job.

16. (Optional) Wait until the laser has reached a stable state.

17. Run the job.