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Knee: sets the knee point and slope for video signal compression to prevent over-exposure by limiting signals in high intensity areas of the subject to the dynamic range of your camera, it adjusts the contrast of a picture. Bill Mills: On the SHIL, we tend to not use it. The TIFF correction that gets done on the raw images seems to be good enough.
Before Starting:
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1.Disable the motor that moves the camera. In the IMS control panel select Motion and then Drive Disable from the dropdown menu (Figure 20). The user can now manually move the camera to the desired spot.
2. Back in the IMS control panel go to Instruments > JAI Camera Settings (Figure 21).The lights turn on automatically when the JAI Camera Setup window opens.
3. Select the Rates and Exposures tab (Figure 22).
There are four main areas in this window:
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You will notice the histogram and profile graphs roughly overlay one another.
6. Select the Lights tab (FIGURE XXFigure 23). Select Lights OFF All Banks. The lights will now turn off
Figure 23. Lights information window
7. Select the Gains-Black-Shade-Flat tab (Figure 24).
- White Balance Gain Correction:
- Pixel Black Auto Correction: The pixel black level represents extra energy in the camera independent of a light source and is a consistent pattern in the sensor. To correct for this the light source must be turned off, the lens cap put on, and the camera internal correction circuit collects a few lines of data. An average is taken across the line, and pixels are either added to or subtracted from in order for each pixel to have the average value. (Manual Reference)
- Shading Correction - Flat Method -: Shading effects can come from an uneven distribution of light and along the outer edge of the camera lens. Shading is corrected for by averaging the signal across a group of eight pixels to represent the line.
- Pixel Gain Correction - Flat Method -: Each pixel has a different response to a fixed light source. To correct for this non-uniformity a couple lines of data are calculated (with the lights at no more than 80% of max) and the average response of the pixels are calculated. Then each pixel has a correction factor applied to bring all pixels to the average level. The Pixel Gain Correction also corrects for some shading effects and should be done after the shading correction.
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2. Next, physically move camera/lights over the color standard (Figure 25).
3. Use courser to draw rectangle around the white field in the field of view of the camera (top right window). The red, green, and blue pixel values reflect the values inside the rectangle. If no rectangle is drawn the values will reflect the entire image. In the lower right window, you will see the color lines. If the lines are angled (left to right or right to left), move the color standard to line it up in the holder. The lines might be drifted out of the window/field of view.
4. Click on the Charts tab (Figure 26). Click on a color box and the manufacturer provided red, green, and blue values will populate. This provides a way to compare expected values with measured values and allows the user to make additional adjustments.
5. Click in the white box to see what the values should be. Compare those values with the values recorded by the camera in the upper right window. If the values do not match there are two options to correct:
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2. In the main IMS Panel select Motion > Drive Enable to re-enable the motor (Figure 27).
3. Go to IMS Main Panel Select DAQ > Image Capture Setup . (Figure 28). In this window confirm that speed is set lower than the speed calculated by the Line Trigger Interval (typically 8.33 cm/sec). Current speed setting is 7.0 cm/sec
Take an Image
1. In the IMS Main Panel click Start and the Sample Information Window will open (Figure 29)
2. Put cursor in the 'Scan' box and scan the STND COLOR and LIG label posted on the track above the desk (Figure 30).
Figure 30. Standard label to scan MacBeth Color Checker
3. Check the ColorChecker Standard box in the lower left corner (Figure 31). This produces a raw TIFF image without corrections applied.
4. Click Take A Picture in the lower right corner. The lights will turn and image the standard.
5. Adjust the green crop box the image to include all the ColorChecker color squares (Figure 32).
6. When satisfied with the crop box click Crop Image and then the green Save button. A new Sample Information window will pop up. Click Cancel to close out of the window.
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1. In the IMS Main Panel go to Instruments > CAMERA: IMAGE Correction (Figure 33)
2. The main Image Correction Window opens (Figure 34). Make sure, TIFF correction is selected. Always select and process TIFF before JPEG.
The Image Correction Window allows users to compare a test image of the standard with known values of the standards. There are three main areas in the window:
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2. Click Open Test Image and navigate to the ColorChecker Standard Image just taken. Select the TIFF file (Figure 35).
3. The entire image will load into the Original and Corrected panel but for this application we only need the color squares. Click on the square tool next to the Original panel and draw a box around the color squares in the image (Figure 36).
4. Click 4. Click Crop. Now just the color squares are seen in the Original Panel. The new cropped image will also update in the Corrected panel.
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7. Now we will be using the gray-scale color squares, outlined in red below, to check and compare RGB values (Figure 37). The goal is to get the corrected image grey scale RGB values as close as possible to the ColorChecker Manufacturer gray scale RGB values.
Figure 37. Gray scale color squares in Color Checker box
8. In the BCG Correction Window select the TIFF Correction tab (Figure 38). In the large graph window on the left select the Uncorrected Image tab.
- RED Poly / R residue:
- GRN Poly / G residue:
- BLU Poly / B residue:
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1. Take the MacBeth Color Checker Standard and place on SHIL Imaging Track
2. Click Start in IMS (Figure 39).
Figure 39. Sample Information Window
3. In the Sample Information window, check the box for Color Checker Standard (Figure 40). Checking this box produces an uncorrected image. Click back in the Sample Information bar and scan the Color Checker Label mounted on the track behind the computer.
Figure 40. Color Checker box outlined in red and selected
4. Click Take an Picture
5. Adjust green crop box as necessary. When satisfied select Crop Image and then Save ImageImage (Figure 41)
Figure 41. Crop and Save Window
6. Close out of the Sample Information Window. In the IMS start area go to Instruments > JPEG CorrectionCorrection (Figure 42)
7. The main window opens (Figure 43).
Figure 43. Main Image Correction Window
8. On the 8. On the right side of the screen select Open Test Image. The IMAGE folder will appear. Select the Image just taken. Make sure to select the .tif image and not the .jpg. With the mouse, hoover over the file and check the extension is .tif. Select the appropriate file and click Open Open (Figure 44). As of writing this, keep TIFF Corection selected while opening Test Image, will receive an IMS error message if select JPEG Correction and then try to load in test image
Figure 44. Selecting Appropriate test image. Callouts to button and .tif image
9. The image loads into main window in the Original section (Figure 45)
Figure 45. Test Image loaded into Original window
10. Now select JPEG Correction Mode (Figure 46).
Figure 46. JPEG Correction selected
11. With the square tool selected draw a box around the color squares (Figure 47). This creates a crop area to focus in on the color boxes. Select crop when the box looks about right. For now the box can be approximate. 
Figure 47. Crop Box drawn around test image
12. With the square tool still selected, draw another box around the squares (Figure 48). This time get the green box very close to the edge of the colored squares. Small white boxes will appear in the color squares. Adjust the green rectangle so the white boxes are approximately in the center of the squares.
Figure 48. Crop box drawn with white boxes centered in color squares
13. In the BCG Correction Window, make sure JPEG Correction is selected. Adjust the Brightness, Contrast, and Gamma Settings. The Corrected color squares will update as the settings are changed.
14. The Applied Corrections Graph should be a straight line and the ROI Corrected Box should have values near 250. These may change depending on the instance of extreme extreme colors, extremely white or extremely dark cores, in which the settings may have be tweaked more to get a user friendly consumer image.
LIMS Integration
Sample and Analysis Components
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