SHIL Calibration Check (Quick Guide)

NOTE: in development, figures to be added

Written by Sarah Kachovich

The following two steps are designed for technicians to check the SHIL’s calibration and to determine if it needs to be adjusted. The calibration check is required to be done at the start of every expedition prior to receiving the first core. If adjustments to the calibration are needed, please see the ‘Advanced SHIL Calibration Guide’.

Step 1: Determine the scan rate for the expedition

1. Talk to your science party to determine what scanning parameters (F/stop and scan rate) they wish to use. A typically scan rate has been between 8-10 cm per second. Note, with the new, brighter LED lighting system, faster scan rates can be achieved compared to expeditions prior to Expedition 390C.

2. Compare the current scan rate to the requested rate.

   1. Launch ‘IMS’ on the SHIL computer, click on the ‘DAQ’ tab and open the ‘Image Capture Motion Setup’ window.

   2. The speed (Fig. 1) of the camera will be in the first box. If the values need to be changed to match the requested values by the science party, please proceed to the ‘Advanced SHIL Calibration Guide’ as you will need to do a full calibration. If the values match, close the ‘Image Scan Setup’ window and proceed with the ‘SHIL Calibration Check (Quick Guide)’.

3. Check the trigger interval rate to see if the values are suitable for the scan rate.

   1. Click on ‘instruments’ tab and open the ‘JAI Camera Set-up’ window.

   2. Turn the lights off IMMEDIATLY by clicking 'Lights OFF' (Fig. 2.1). The lights produce a lot of heat and can quickly burn anything underneath them if they remain stationary for too long. (Link to LED lighting system)

   3. Click ‘Rates and Exposure’ tab (Fig. 2.2)

   4. Check that the ‘Max Image Scan Speed’ (Fig. 2.3) is equal to, or slightly less than the designated ‘Scan Rate’.

   5. Again, if the values need to be changed to match the requested values by the science party, please proceed to the ‘Advanced SHIL Calibration Guide’ as you will need to do a full calibration. If the values match, close the ‘JAI Camera Set-up’ window and proceed with the ‘SHIL Calibration Check (Quick Guide)’.

   6. Close the ‘JAI Camera Set-up’ window once done

Step 2: Assess the SHIL scan

1. Place the 3D standard on the track (Fig. 3: see the ‘Advanced SHIL Calibration Guide’ to learn more about this standard and where it is kept)

2. Scan the standard:

   1. In the IMS program, click 'Start' and scan the color standard barcode (Fig. 4)

   2. You must check the 'Color Checker Standard' box (Fig. 5) to scan without applying any post scan acquisition corrections.

   3. Scan the standard by clicking 'Take a Picture' button

   4. Once the image is scanned, click ‘Crop’ and save it. Hit ‘Cancel’ when you are promoted to scan another section.

3. Prepare the scan to assess the current image correction values. If you can achieve a good image by either adjusting, or better yet, keeping the same, values in the following steps, you will not need to adjust any of the camera settings in the ‘JAI Camera Set-up’ window in the ‘Advanced SHIL Calibration Guide’.

   1. Under the 'Instruments' tab, open the 'Image Correction' window

   2. Open either the TIFF or JPEG test image you just took (Fig. 5a), located in the C:/DATA/IN/IMAGE folder. It does not matter if you use the TIFF or JPEG for the post scan acquisition corrections.

   3. Draw a ROI rectangle around the Color Checker in the 'Original' window (Fig. 5b)

   4. Click 'Crop' (Fig. 5c)

   5. Re-draw the ROI and ensure the ROI squares are in the center of each of the colored patches (Fig. 6a). Do not crop again.

1. Assess the TIFF corrections:

2.  

   1. Click on the 'Tiff Correction Mode' button (Fig. 6b)

   2. Click on the 'Uncorrected Image' tab on the graph (Fig 6c).

   3. Click on the 'Tiff Correction' tab (Fig. 6d) and assess the shape of the graph. Adjust the RGB polynomials so that each ‘RGB Residues’ goes to the lowest value (Fig 6c) while keeping a liner relationship. If the graph is too curved, you will need to go the ‘Advanced SHIL Calibration Guide’ and adjust the scanning conditions. You want to achieve an image with good brightness, where the image has true saturation and not too washed out (see TIFF corrections cheat sheet).

3. Assess the JPEG corrections:

4.  

   1. Using the same image, click on 'JPEG Correction Mode' (Fig. 7a)

   2. Click on the 'Applied Corrections' tab on the graph (Fig. 7b)

   3. Click on the 'JPEG Correction tab' (Fig 7c)

   4. Here, you can adjust the Brightness, Contrast and Gamma to improve the quality of the JPEG images. You want to look at both the graph and the RGB values of the colored patches in the three windows (Fig.7d).  You want to achieve an image with good brightness, where the image has true saturation and not too washed out (see JPEG corrections cheat sheet). If you can achieve good a TIFF and JPEG images with the color standard, click 'Save' and you have finished the ‘SHIL Calibration Check (Quick Guide)’. If you cannot get a good image or if there are any artifacts in the image (streaks, color aberrations, etc.) you will need to go through the ‘Advanced SHIL Calibration Guide’.

Optional step:

1. Check the final scan:

2.  

   1. To double check your calibration under the same scanning conditions as the scientists see, scan an image of the 3D standard without the 'color checker' box.

   2. Crop the image and save it

   3. Open the TIFF and JPEG in Photoshop. Images located in the C:/DATA/IN/IMAGE folder.

   4. Visually examine each file you just preformed to ensure the colors, neutrals, mid-tone and contrast are true to the real values, and that the scan is free from artifacts. Use the eyedropper tool in photoshop to see the values of pixels (Fig. 8).