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How do you troubleshoot and maintain a microarray scanner?

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A microarray scanner is a device that detects and measures the fluorescence signals from a microarray, a collection of microscopic spots of DNA, RNA, or proteins attached to a solid surface. Microarrays are widely used in bioengineering research and applications, such as gene expression analysis, genotyping, and biomarker discovery. However, a microarray scanner can encounter various problems that affect its performance and accuracy, such as dust, alignment issues, background noise, and signal intensity variation. Therefore, it is essential to troubleshoot and maintain a microarray scanner regularly and properly. Here are some tips and steps to help you do that.

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Iyeswaria K.

1 Clean the scanner

One of the most common causes of poor microarray scanning results is dust or dirt on the scanner components, such as the glass slide holder, the lens, the mirrors, and the filters. Dust can block or scatter the laser beam and the fluorescence emission, resulting in low signal intensity, high background noise, or uneven spots. To clean the scanner, you should follow the manufacturer's instructions and use the recommended cleaning materials, such as lint-free wipes, compressed air, and optical cleaning solution. You should also wear gloves and avoid touching the optical surfaces with your fingers. You should clean the scanner before and after each scanning session, and check for any visible dust or stains.

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Iyeswaria K.
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In my experience, the major cause of technical errors in scanning micro array scanner are accumulation of dust, hence periodic cleaning with soft microfiber based cleaning brushes can help us maintain the instrument functional for a long period of time.

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Jayita Goswami

Cell and Molecular Biologist
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First and foremost, test the bandwidth of the optics and their positioning. Run a proxy experiment. Use all the chemicals and their wavelengths to subtract the background. Every single experiment, you can subtract that value. You have to subtract the plate/polymer's absorbance or luminescence too. Afterwards, you can trust your data.

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2 Calibrate the scanner

Another important step to ensure the optimal performance of the microarray scanner is to calibrate the scanner settings, such as the laser power, the PMT (photomultiplier tube) gain, and the focus position. These settings affect the sensitivity and resolution of the scanner, and they may change over time due to environmental factors, such as temperature and humidity, or mechanical wear and tear. To calibrate the scanner, you should use a calibration slide provided by the manufacturer or a standard microarray slide with known fluorescence values. You should adjust the settings until you obtain the desired signal intensity, dynamic range, and spot quality. You should calibrate the scanner at least once a month, or more frequently if you notice any changes in the scanning results.

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Iyeswaria K.
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Calibration is the major thing that needs to be addressed before starting any experiment. Having a standard reference either provided by the manufacturer or one custom prepared by us based on known data of our previous experiment on the same instrument are some of the ways i have calibrated my instruments.

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3 Validate the scanner

After cleaning and calibrating the scanner, you should validate the scanner performance by scanning a test slide with a known microarray pattern and comparing the results with the expected values. This step can help you identify any errors or inconsistencies in the scanner output, such as missing spots, distorted spots, or inaccurate signal intensity. You should use a validation slide provided by the manufacturer or a quality control microarray slide with a standard reference sample. You should analyze the scanned image using a software tool that can calculate the spot metrics, such as the signal intensity, the signal-to-noise ratio, the spot diameter, and the spot uniformity. You should compare these metrics with the manufacturer's specifications or your own criteria, and determine if the scanner meets your expectations. You should validate the scanner after each calibration, or whenever you suspect a problem with the scanner.

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4 Troubleshoot the scanner

If you encounter any problems with the scanner during or after scanning, such as low signal intensity, high background noise, uneven spots, or image artifacts, you should troubleshoot the scanner by following a systematic approach. First, you should check the scanner components and connections, and make sure they are clean, secure, and functional. Second, you should check the microarray slide and the scanning parameters, and make sure they are compatible, appropriate, and consistent. Third, you should check the scanning environment and the scanner software, and make sure they are stable, updated, and configured correctly. Fourth, you should consult the manufacturer's manual or support service, and follow their troubleshooting guidelines or recommendations. If none of these steps resolves the problem, you may need to contact the manufacturer for repair or replacement.

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5 Maintain the scanner

To prevent or minimize the problems with the microarray scanner, you should maintain the scanner regularly and properly. This includes following the manufacturer's instructions and recommendations for the scanner operation, storage, and service. You should also keep a record of the scanner usage, cleaning, calibration, validation, and troubleshooting, and monitor the scanner performance over time. You should also follow the best practices for microarray handling, preparation, and scanning, and avoid any factors that may damage or degrade the microarray quality, such as contamination, humidity, light exposure, or temperature fluctuations. By maintaining the scanner, you can extend its lifespan, improve its reliability, and enhance your microarray results.

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Iyeswaria K.
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Record of people who used the scanner and their sample details are some of the key things that need to be addressed in a sign in form that is placed next to the scanner. When its time for maintenance, and in case of troubleshooting, these data come in handy to detect the bug.

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6 Here’s what else to consider

This is a space to share examples, stories, or insights that don’t fit into any of the previous sections. What else would you like to add?

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How do you troubleshoot and maintain a microarray scanner?

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1 Clean the scanner

2 Calibrate the scanner

3 Validate the scanner

4 Troubleshoot the scanner

5 Maintain the scanner

6 Here’s what else to consider

Bioengineering

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