Thursday, May 16, 2013

How to Choose a Microarray Scanner

Here is my current list of characteristics to define what I consider the best microarray scanner to match any 1 or two color application for both in-situ and ex-situ manufactured microarrays. Adhering to this criteria will guarantee that end users buying a microarray scanner will be compatible with all current and future applications for standard industry sized microarrays.

The list is as follows:
  • One micron resolution and adjustable to larger feature (spot) sizes. Currently the Innoscan 900 system at 1 micron resolution has the highest resolution system of any microarray scanner available. It can also be customized down to 0.5 micron under a special order. Resolution is important for reliable data acquisition and scanner resolution should be adjustable to read larger and smaller spots as needed. Images used in analysis at 10um resolution have a much smaller file size than 1 um resolution files. Some scanners lack sufficient resolution to read very high density in-situ manufactured microarrays. Sufficient numbers of pixels must be in the microarray image for reliable quantification of data. 1 um resolution assures compatibility with all current and future microarray scanning requirements as feature sizes on microarrays get smaller.
  • Adhere to the microscope slide size substrate microarray format, the current standard in the industry. Adhering to this standard allows a single user to get the microarrays they need from multiple vendors. Well known microarray manufacturing organizations that support this standard are Arrayit, Agilent, Thermo Fisher, Life Technologies, and many others. Companies that do not support this format include Affymetrix and Illumina and do not adhere to standards that have been set and in place since 1995!!! This pushes end users into needless expense to purchase equipment they don't need. Arrayit adheres to the standard in support of the entire scientific community world wide with a truly open platform.
  • A microarray scanner that adheres to the open slide substrate platform design should scan the top of the slide to be compatible with any slide type. Systems that scan through the glass have limited their utility, they cannot scan non-transparent substrates such as silicon wafers, mirrored or other coated signal amplification surfaces, nitrocellulose, nylon and PVDF membrane coated slides.
  • Images from the scanner should be 16-bit gray scale file files. This format allows for highly quantitative results that can be opened by a variety of image quantification programs, including open source freeware programs. Some scanners do not adhere to this standard, thus making the images difficult if not impossible to analyze on "open" system software.  Newest development as of 2013 is compatibility with 20-bit extended dynamic range protocols.
  • Image quantification files should be in a txt format, fully exportable into any downstream data analysis software.
  • Scanner should be a networkable device to connect multiple users to a single resource. Outdated systems using slow computer connections that not only slow down data acquisition speeds, they also cannot connect multiple users to a single system. Our Innoscan systems are network devices to allow multiple users on a single system. with the ability of security through administrative network tasks to lock out unwanted users.
  • Acquisition and analysis software should run on any operating system including Linux, or Windows. What is probably considered the most "open" computing system is Linux, with very good freeware OS being readily available. Both Windows 7 and Linux provide true 64 bit operating systems and maximum available RAM for high performance high resolution image acquisition and analysis.
  • Microarray scanners should include dynamic auto focus coupled with confocal design for superior signal to noise ratio and more reliable detection of low signals. Non-confocal microarray scanners that rely on a wide field of view for focus introduce unnecessary noise into the data.
  • Software should be easy to use. A new user, without reading a manual, should be able to start acquiring images within a few minutes of being introduced to the system by an experienced user.
  • Scanning movement of the slide should empower the fastest scanning times possible without unnecessary vibration of the hardware. Vibrations introduce noise in all electronic systems. The Innoscan series of scanners have a proprietary and patented slide movement system for both speed, accuracy and limited vibration.
  • Lasers inside the scanner must be held at a constant temperature. Systems that do not control laser temperature have non-linear fluctuation of laser power being used in scans. Power feedback software algorithms based on temperature cannot match the linearity of constant temperature control. Innoscan systems use internal peltier devices to maintain perfect operating temperatures of the lasers. This also helps to increase lifespan of the lasers and no wasting valuable lab time waiting for lasers to reach operating temperature.
  • Bar code reading is extremely useful for both operational efficiency accurate data tracking.
  • An option that is very nice to have is a slide autoloader. Innoscan systems can come with autoloaders.

I look forward to any feedback someone may have to this list. Please email me at