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1. Grab the calibration standard and remove from liner (Figure XX19). Calibration Standard is located in drawer PP-2B.
Figure XX19: The calibration standard in its cover.
2. Put the Calibration Standard in the track (Figure XX20). The color square must be oriented as pictured below.
Figure XX20: Color standard in track in correct orientation.
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4. Scan the STND Color label on the aluminum track behind the monitor (Figure XX21). Check the ColorChecker Standard box. With this box selected no corrections are applied to the image so we are able to assess the raw image quality.
Figure 21: Left, sample information screen with ColorChecker box checked. Right, standard barcode being scanned.
5. Click Take A Picture.
6. When the image has finished click Crop and then Save. We user the uncropped image so the crop here is not important.
7. On the main IMS panel select Instruments and Camera: Image Correction (Figure 22).
Figure 22: Image Correction command selection.
8. Select Open Test Image and select the image you just took (Figure 23). It does not matter if the JPEG or TIFF file is loaded - at this point not tested to confirm it doesn't matter if a jpeg is loaded and used to perform the tiff correction.
Figure 23: Image Correction Window. Steps are indicated in the screen. 1. Open the Scan 2. Draw a box around ColorChecker Squares 3. Click Crop.
9. The image loads into both the Original and Corrected windows. With the rectangular box selected, draw a box loosely around the color checker card as illustrated above, then click Crop. Draw a box around the Color Checker squares again and this time making sure to only have squares in the box. This time white squares will appear inside each square. Adjust the box to get those white squares close to the center of the color squares.
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1.Check the TIFF Correction (Figure XX24). Select TIFF Correction Mode and look at the Uncorrected Image tab. The goal is to have line as straight as possible. Adjust the Red, Green, and Blue polynomial orders to achieve the lowest residual value while still keeping a relatively straight line in the graph.
Figure 24: Steps for Tiff Correction illustrated on image. 1. Redraw box on color squares. 2. Select Tiff Correction Mode. 3. Put graph on Uncorrected Image. 4. Select Tiff Correction to view polynomial order. 5. Adjust polynomial order. 6. Check graph for linear relationship.
2. Check the JPEG Correction (Figure 25). Select the JPEG Correction Mode in 2. Check the JPEG Correction (Figure XX). Select the JPEG Correction Mode in the top right of the screen, JPEG Corrections in the bottom right box, and look at the Applied Corrections tab. We want a linear relationship between the measured and given values. Adjust the Brightness, Contrast, and Gamma levels to achieve this. Each setting adjusts the line in different ways and there are many different ways to adjust the values to achieve a linear relationship
Figure 25: Steps for JPEG Correction illustrated on image. 1. Select JPEG Correction Mode. 2. Select Applied Corrections tab on graph. 3. Select JPEG Correction to see Brightness, Contrast, and Gamma Corrections. 4. Adjust Brightness, Contrast, and Gamma corrections. 6. Check graph for Linear Relationship. 7. Check the boxes in the Color Checker and compare to RGB values in corrected image.
3. If the values all look good and there are no streaking issues in the images, you can click Save and no further adjustments are needed. However if you have determined it doesn't look good, click cancel and you can proceed to the following section and calibrate.
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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 1926). The user can now manually move the camera to the desired spot.
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2. Back in the IMS control panel go to Instruments > JAI Camera Settings (Figure 2027). The lights turn on automatically when the JAI Camera Setup window opens.
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4. The lights will turn on when the JAI Camera Window opens. Due to the intensity and heat produced by the LEDs it is best to turn off the lights until ready. Turn off the lights in the software window (Figure 2128) or with the physical power switch located behind the monitor (Figure 2229). Note if the lights are turned off by the harware switch, the lights cannot then be turned on the software command.
Figure 2128: Software commands to turn the Lights On or Off.
Figure 2229: Hardware Switch to turn power on or off to the lights located behind monitor.
Color Balance the Camera
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1.Select the Gains-Black-Shade-Flat tab (Figure 2330).
Figure 2330: 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 2431). You will notice all values in the Master and Black gains to zero.
Figure 2431: The five clear and remove buttons of interest are outlined in red.
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1.Select the tab RATES and EXPOSURE (Figure XX32).
Figure 32: Rates and Exposure tab with chronological steps on the screen
2. On the Green Lock control select OFF (Figure 32). The other exposures are now adjustable.
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5. Click the Start Grab (Figure 3632).
6. Turn on lights, but only keep them for ~20 seconds and then turn off for ~ 1 minute.
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2. Take the lens cap (Figure 2933) and place on lens (Figure 3034). The lens cap is located in drawer PP-2B.
Figure 2933: Lens cap for the camera
Figure 3034: Lens Cap being put on camera
3. Click the Pixel Black Auto Correction. The RGB lines in the Profile graph should be uniform (Figure 3135). (Note: half the time a separate window window pops up to confirm lens cap is on, then user clicks 'Proceed' to apply correction. Inconsistency reported in Confluence)
Figure 3135: Grab and Profile after the Pixel Black Correction applied.
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- Place the gray silicone mat on the tray make sure that it is level and perpendicular to the camera’s axis. The mat should be positioned at the height of the core surface. This is an important step. If the mat is placed closer to the camera your calibration will be off.
- Turn on the lights, with the same method used to turn off the lights, and move the camera over the gray mat.
- Unfocus the lens on the camera just a little bit (Figure 2536). Look at the Profile graph and rotate the lens’ focus until the RGB lines are smooth. de-focus the lens until the RGB line on the Profile graph just become smooth and no more (but still variable)
Figure 2536: The lens being unfocused.
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4. Now move the camera over the gray card (Figure 2637). The RGB lines should appear “bowed” evenly across profile and centered in the image. If not check the orientation of the grayscale card. This very important!
Figure 2637: Grayscale card are corresponding RGB Profile visible.
5. 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 2738).
Figure 2738: Grab and profile after the Shading Correction has been applied.
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2. Click the Pixel Gain Correction - Flat Method button and move the camera very slowly back and forth over the mat. 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 are the same (may not be equal to each other) (Figure 2839).
Figure 2839: Grab and Profile after the Pixel Gain Correction has been applied.
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1.Go to Motion > Drive Enable, to re-enable the motor (Figure 3840).
Figure 3840: Drive enable control highightedhighlighted.
2. Go to IMS Main Panel Select DAQ > Image Capture Motion Setup (Figure 3941). In this window confirm that speed is set lower than the speed calculated by the Line Trigger Interval
Figure 3941: Image Scan Setup Window.
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4. Scan the STND Color label on the aluminum track behind the monitor (Figure XX42). Check the ColorChecker Standard box. With this box selected no corrections are applied to the image so we are able to assess the raw image quality.
Figure 42: Left, sample information screen with ColorChecker box checked. Right, standard barcode being scanned.
5. Click Take A Picture.
6. When the image has finished click Crop and then Save. We user the uncropped image so the crop here is not important.
7. On the main IMS panel select Instruments and Camera: Image Correction (Figure 43)
Figure 43: Image Correction command selection.
8. The main window opens. On the right side of the screen select Open Test Image. Open the image just taken (Figures Figure 44). It has been mentioned that it doesn't matter if you load in the jpeg or tiff, not tested yet
Figure 4544: Open Test Image Window with all images displayed.
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The main Image Correction window opens (Figure 4345). Note the three main areas in the window:
Figure 4345: Image Correction Window.
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1.Make sure TIFF Correction Mode is selected in the upper right corner and the TIFF Corrections tab is selected in the bottom right corner (Figure 4446).
Figure 4446: Tiff correction Mode button and Tiff Correction tab both highlighted in red.
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3. Again create another selection rectangle over the image but do not release the mouse. Move the lower corner of the rectangle until small white boxes appear over the color squares. Make sure the boxes are in the center of the squares. Release the mouse. The pixels in the squares will be averaged and used for the RGB values in the calibration (Figure 48). (not quite how it works right now, white squares don't show up until mouse is released, error reported in confluence).
mouse is released, error reported in confluence).
Figure 48: Steps for Tiff Correction illustrated on image. 1. Redraw box on color squares. 2. Select Tiff Correction Mode. 3. Put graph on Uncorrected Image. 4. Select Tiff Correction to view polynomial order. 5. Adjust polynomial order. 6. Check graph for linear relationshipFigure 48: Final crop square drawn around color squares.
4. Look in the TIFF Correction tab and set the LUT polynomial order values for the RGB channels. Adjust these values to create the lowest residual error with the smoothest curve in the UNCORRECTED image tab. Should be around 4. Make sure that the curve does not wave about if it does the order values need to be lowered. Also check the corrected ROI and MacBeth values should be very close. Make sure that the white does not exceed the MacBeth value. If you are unable to produce a reasonable correction curve, it may be necessary to redo your white balance correction and start over.
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1. Select JPEG Correction Mode (Figure 5649).
Figure 49: Steps for JPEG Correction illustrated on image. 1. Select JPEG Correction Mode. 2. Select Applied Corrections tab on graph. 3. Select JPEG Correction to see Brightness, Contrast, and Gamma Corrections. 4. Adjust Brightness, Contrast, and Gamma corrections. 6. Check graph for Linear Relationship. 7. Check the boxes in the Color Checker and compare to RGB values in corrected image.
2. In the BCG Correction Window, select JPEG Correction. Adjust the Brightness, Contrast, and Gamma Settings. The Corrected color squares will update as the settings are changed.
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