Multiple Scanner Acquisitions
Using Chitraka, microarray images acquired from different scanners can be analysed. Moreover, Chitraka supports specification of scanner resolution from different scanners along with with arraylist files such as GAL for automatic grid computation and layout.

Multiple Channel Experiments
Chitraka supports analysis of two-dye Cy3/Cy5 image experiments. Chitraka works on the composite image generated from the two-channel images for accurate computation of spot boundaries. The spot boundaries are then used on individual images for computing accurate foreground / background values of spots.

Imaging Operations
Chitraka supports imaging operations such as contrast, brightness, sharpness for user-level quality control of images. These operations alter the state of the images in the view, but do not affect the original images. In addition, default normalization of images allows certain portions of the image to be enhanced in quality.

Automated Gridding/Segmentation
Chitraka provides automatic as well as semi-automatic techniques in identification of features accurately and quickly. Chitraka allows direct loading of arraylist files such as GAL ( extensible to other types), and automatic inference and layout of the grids from information in the file. Next, the automatic grid tuning facility, allows for tuning the grids and tightening the boundaries around individual feature blocks. A second level of tuning for sub-grids also allows finer tuning of sub-grid lines between spots, which are otherwise extremely difficult for manual editing.

Accurate feature detection
Once the grids are placed accurately over the blocks using the above techniques, the spotting process identifies individual spot boundaries accurately and quickly. Chitraka allows for detection of doughnut shaped spots, where the center of the spots may have some background. These are automatically taken care of by algorithms in Chitraka.

Robust Spot Statistics
Chitraka computes foreground and background statistics taking outliers into account. In addition, advanced background correction methods account for extraneous noise from adjacent spots also.

Interactive Graphical User Interface
Chitraka has interactive user interface (GUI) and all steps in the image analysis process can be executed with only a few mouse clicks. Chitraka allows users to work with multipe images in individual workspaces including multi-dye images. Each workspace is assigned an image, a spreadsheet view and a graphical view for analysis of values. In addition, Chitraka allows advanced grid/grid navigation techniques for multi-grid images. It further allows automatic tuning of grids and sub-grids block by block, as well as for complete images. Users have editing options for grids, line segments, and also individual spot editing. Chitraka also provides individual spot views in a separate window along with all the relevant analysis values, both for single and multi-dye images. Feature analysis of images are then displayed in SpreadSheet tables that allow graphical visualization and manipulation.

File Formats
Chitraka can read array list formats such as GAL. It can be easily extended to read any additional type of formats.

System Details
Available as a Desktop version on Windows. Minimum memory required 256MB.