Fix Lighting

Correct Background

Hamamatsu line scanning CCD Time Delay Integration (TDI) cameras are used in the Illumina HiSeq2500 sequencing system. The pixels in these cameras are arranged in a line in groups of 256 or 512 pixels (depending on the model). Each group has a different dark pixel value which is corrected to create a flat background.

Register Channels

The HiSeq images 4 emission channels simultaneously, however the images from these 4 channels are not perfectly aligned and differ from machine to machine. Machine specific sub pixel channel shifts are precomputed during machine commissioning using phase cross correlation. Channel shifts are applied using a rigid affine transformation.

Stitch Tiles

Since the HiSeq uses line scanning TDI camera, image tiles are arbitrarily long in the row dimension (Y axis) and have a fixed column width (X axis) of 2048 pixel. Tiles can also optionally overlap a specified pixel width across the X axis during image acquistion. Tiles are stitched across the X axis with overlapping regions removed.

Processed Image

Input

Zarr store of raw images

Output

Zarr store of processed images

Logs

Script log Dask performance report