Inside VisiGene. Parallel programming constructs: Para: executes in parallel on all items in a collection. Flow: marks a function as having no side effects.

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Presentation transcript:

Inside VisiGene

Parallel programming constructs: Para: executes in parallel on all items in a collection. Flow: marks a function as having no side effects.

Virtual Microscope Galt’s bigImage.html file Image is saved at full size, 1/2 size, 1/4 size, and so on down to 1/64 size. Broken into 500x500 pixel tiles. Uses JavaScript to fetch just the tiles needed for the part being displayed.

A whole lot of tiles… Allen Brain images are ~15000x15000 Generate 500 tiles each Overall have ~3 million tiles covering images Have at least one image for genes.

The JPEG 2000 Challenge Allen uses JPEG 2000, which is based on wavelet compression rather than discrete cosine transform of regular JPEG. JPEG 2000 not widely supported yet. After much experimentation with what was available on net, Galt found ECW toolkit, which is very nice, fast and free. The program based on the ECW toolkit converts an Allen JPEG 2000 images to tiled JPEG at rate of ~1/minute on a single CPU.

VisiGene Loading in General Get images and data from contributors. Write a program to convert data into a standard.ra/.tab file format. Create image tiles with vgPrepImage Load.ra/.tab file into relational database with visiGeneLoad Associate known genes with knownToVisiGene View with hgVisiGene

Near Term Additions Updating Jackson Labs images. (Over 6 months old) Load frog images from Harland lab Bring in zebrafish images from zfin

Possible Long Term Projects Making it so that users can submit images over the web. Allowing contributors to normalize and crop images in their own sand box before making images public.