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The laboratory technician calibrates the system when needed by adjusting camera settings and analyzing an imaged XRite Color Checker Standard (MacBeth card). The current light system obtains nearly uniform illumination intensity from the core’s surface (half or whole round) to the bottom of the liner by a combination of high intensity, overlapping large diameter light source, close coupling to the imaged surface and the “line” image plane. The bottom edge of the brass led mount should be set between 2 and 4cm from the image surface. Note, any height change to the lights requires re-calibration. Heat is removed from the LEDs and transferred to the surrounding air via the copper heat pipes and is cooled with mini fans. While the copper rods can get hot they are not a burn hazard. However they are very delicate and bend at the slightest touch, so use care when working with the camera lens. For more detailed information on the theory behind the calibration please refer to the /wiki/spaces/LN/pages/7338174348 for further reading. Maintain temperature of the lights at 30-40 °C during calibration. LED's of temperature is located above the camera. During a section scan the temperature ranges between 30-36 °C.
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- Physically set the camera at the correct height and focus . See Camera Height and Focusing.
- Set the saturation range for each channel of the CCD while maintaining the white balance between these channels for neutral colors. See Setting Exposures and Setting Gains.
- Correct for uneven lighting, dark noise and pixel flatness. See Pixel Black, Shading and Flat Corrections.
- Calibrate and create a correction LUT for each RGB channel. See Image Calibration.
The first three steps are done using the JAI JAI Camera Setup Utility. Before opening the utility it is best to disable Motion Control so that you can move the camera by hand.
Disable Drive:
- In the IMS control panel select Motion and then Drive Disable from the dropdown menu (Figure 19). You will have to move the camera by hand for the calibration, disabling the motor allows manual movement of the camera on the track.
2. Open JAI Camera Setup utility:
In the IMS control panel click Instruments > JAI Camera Settings (Figure 20). The lights turn on automatically when the JAI Camera Setup window opens.
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The goal is to set the across image pixel pitch with a focused camera. Warning this can be very tedious and requires two people.
1) . Move the camera so that it is scanning just the centimeter marks on the QP 101 card (Figure 22). Also, it is important that the QP 101 card is mounted straight so that the scale lines are parallel to the direction of motion.
Figure 22. QP 101 card showing centimeter marks for pixel pitch calibration.
2. On the screen you will see this..the cm lines and vertical peaks on the Profile graph (Figure 23).
Figure 23. Example of the QP-101 marks and the profile graph.
2) 3. On the Profile graph, drag the purple and yellow cursors to the center of two adjacent peaks near the center of the image. These peaks are the centimeter lines in the QP card.
3) 4. Use the graph controls and expand (zoom) the graph horizontally and you should see this…(Figure 24).
Figure 24. Cursor placement on the QP 101's centimeter marks in Profile graph.
5) . In the expanded view, adjust the cursors so that the are centered in the peak's width (not necessarily the max value).
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You want to achieve a Pixel Delta of 200 pixels/cm (+/-1px) (Figure 25).
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25. Cursor pixel values and span.
6) Change camera height
7) Focus
8) Adjust cursors
9) Check Pixel Delta
10) Repeat steps 6 through 9 as necessary.
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Be careful how you tighten the clamps holding the camera to the T- Slot. Make sure to tighten with even pressure on both sides, if you don't the camera can be offset and you will see the image in the Grab window shift. The camera attachment method is not ideal and should be replace. After performing this process you need to check the home position. When at the home position, the camera should be scanning the edge of the tray where the section is placed against (red strip). If not, you will need to adjust the home switch on the track until it does. An improperly set home switch will affect the placement of the crop window and potentially the offsets assigned to the RGB values! |
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1. Click the Gains-Black-Shade-Flat tab (Figure 2526).
Figure 2526. JAI Camera Setup Window showing the Gains-Black-Shade-Flat tab. The Gains-Black-Shade-Flat tab is outlined in red.
2) . Click the Clear All Gains, Clear Black Gains, Remove Pixel Black Correction, Remove Shading Correction, and Remove Pixel Gain Correction (Figure 26). You will notice all values in the Master and Black gains go to zero.
Figure 26. Remove the corrections and clear gains.
3) Check the camera's f/stop which should either f/16 or f/22 (see Figure 27). Remember that the higher the f-stop the greater the depth of focus. The down side is that a higher f-stops means less light and low light level mean longer exposures - which means slow track speeds for scanning - which could impact core flow in the lab. So on a low recovery expeditions you can afford the longer scan time, so go for f/22 otherwise f/16. If you are doing 360-imaging f/22 is a must. Check with the LO and EPM if you are unsure.
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5) Adjust the Master Back value unit the Green value is near 15. 40 is a good starting point.
6) Adjust the Red Black and Blue Black Gains until the ratio are close to 1 +/- 0.01
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Image striking is caused when used a non-uniform standard for the Pixel Gain Correction correction or just from dirt. Until we found the silicone sheets we would have to defocus the lens to mitigate this issues. If see streaks chack your target material and repeat this correction. |
Pixel Black Auto Correction
1)The new light set up makes adding a lens cap difficult so it has been decided and tested that the pixel black auto correct can be done without the cap (Figure 33). But Ensure the lights are off.
Figure 33. Lens Cap being put on camera - note the lens cap is not needed. Ensure the lights are off.
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Figure 34. Pixel Black Correction applied.
Shading Correction
1) Take the heat resistant gray silicone mat and wooden board from the SHIL calibration drawer. Clean off any dust with a piece of tape (Figure 35). Dust will cause unwanted artifacts in the image. The mat must be clean and flat on the track.
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4) Note for Tech: previously we defocused the lens to preform the Shading correction. That is no longer needed because the silicone mat is even in color/texture.
Figure 35. The Gray silicone mat being cleaned with tape.
5) The RGB lines should first appear “bowed” evenly across profile and centered in the image (Figure 36). If not check the orientation of the gray mat, it needs to be flat and perpendicular to the camera. This very important. A wooden holder was designed to hold the mat, it should be in the SHIL calibration drawer.
Figure 36. Grayscale card corresponding RGB Profile visible.
6) Click the Shading Correction - Flat Method button. This can take a few seconds, don’t click anything else until it is done. The RGB lines should now be flat (Figure 37).
Figure 37. Image grab and profile after the Shading Correction has been applied.
7) Click Lights OFF and wait for temperature to decrease below 35 °C.
Pixel Gain Correction
1) Make sure gray silicone mat is flat.
2) Click Lights ON
3) Click the Pixel Gain Correction - Flat Method button and move the camera slowly back and forth. This averages the pixels and helps eliminate streaking in the image. This will take several seconds, don’t click anything else until it is done. When its done the RGB lines should still be flat and the individual RGB the same, but may not be equal to each other.
IMAGE Calibration (Correction)
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1. Place the 3D calibration standard on track as shown (Figure 10). Be sure to use the XRite Color checker 2019. The color squares must be oriented as pictured below, butted against the red reflection bar.
Figure 38. Color standard in track in correct orientation.
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2. Adjust the Brightness, Contrast, and Gamma levels (Figure 45-1) to achieve a straight line in the Applied Corrections tab and the RGB Corrected values in the Compare tab should have values near 242 for the white square and near 50 for the black. We want a linear relationship between the measured and given values. Each BCG setting adjusts the line in different ways and there are many different ways to adjust the values to achieve a linear relationship. You want to achieve a good image with good brightness, where the image has good saturation and not too washed out. The Applied Corrections Graph should be a straight line and the ROI Corrected box for the color selected (Figure 45-2, 45-3) should have values near the RGB values of the Color Checker STND. These may change depending on the instance of extreme colors, extremely white or extremely dark cores, in which the settings may have be tweaked more to get a user friendly consumer image.
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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 selected.
2. Click Crop and Click Save
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C.2 ColorChecker RGB Values
A link to the Excel Spreadsheet of RGB values calculated from L*a*b* for the Xrite Mini Color Checker is here. L*a*b* was obtained from xrite.com.
C.3 VCD-S Configuration
"Scratch sheets" are printouts of section half images produced by SHIL. The sheet is a LabVIEW VI with embedded images that can print automatically when a user 'saves' an image. The VI is scaled to print SHIL images correctly on 11x17" paper in portrait orientation. The scratch sheet can be customized to include various columns to capture descriptions or drawings on paper. The goal of this guide is to instruct how to use and customize scratch sheets.
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