The Problem

Microarrays are 2-dimensional arrays of spots formed by the deposition of biological samples mixed with reagents. Microarray imaging is used for assaying large number of biological samples using clinical multiplex techniques. Images of the microarrays are captured and analyzed for diagnosis of ailments, genetic disorders, DNA/Protein analysis and genomics. A European bio-medical company wanted Tismo to develop this complex imaging and analysis software on the .NET / C# platform.

The Solution

The microarray reader hardware provided supported for x, y & z axis on which a high resolution camera was mounted. The microarrays are arranged on a plate or a slide. The camera was required to move to different positions on the microarray plate or slide and capture the images of the microarrays. The scanning of wells/slides and image capture was governed by microarray layout definition and physical parameters of the plate. As the microarrays could be of different sizes, one or more images of the microarray had to be captured if the dimension of the microarray was larger than the field of view of the camera. In such cases, images were captured in a known pattern and were stitched together to form a single large image of the microarray. Controlling the movement in the z-axis allowed manual or autofocus operations. Image capture, pre-processing, threshold detection, background correction are performed on the images. The system also provided the ability to place markers on the images so that the markers formed the reference pattern based on which the microarray spot were detected and analyzed. Various parameters including spot size, intensities of the spots (mean, average intensity etc) were collected and displayed. This enabled the user to get instant results from the analysis of the microarray images. The workflow for different types of users such as Research Scientists, Lab Technicians and System Administrators were built into the system. Access controlled operations allowed different types of users to use different workflows. The workflows were constructed with GUI which enabled easy navigation across different parts of the system. For example, research scientists would require fine-tuned image acquisition and analysis parameters and process. The image management (view, recapture, reanalyze etc) support was also built into the system. The system was developed using Microsoft C# on .NET version 3.5 on Windows XP/Vista/7.

The software that includes the image scanning, image capture, image analysis, method editor and view functionality was developed in an iterative development model, with several releases to the market and was completed as per plan.