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[Draft] 2DE-SDE 1st stage of refinement

2D-Refinement Stage I

Buenos Aires, January/2005.
Alejandro F. Reimondo

Introduction

The word done in the last stage was implemented as a minimum working version.
Some alternatives has been discarded while reaching a good solution but without testing all the posibilities of use.
During the next stage it is planned to solve the patologies found and enhance the current version, reevaluating the posibility to use a mix of techniques on the current implementation.
The objetives of the next stage has been planned to reach a complete and robust implementation for Spot detection with automatic correction and inference of most common pathologies (like fused spots and high saturaturated images).

Goals

Seed analysisSaturated images has dark spots, and the contour must be considered to detect more than one spot in the same blob. Also gradient must be scanned to get confirmation of been a spot and not a fracture of the gel.
Also the degree of saturation can be stored in detected spots.
Spot splittingThe procedure to split fused spots must be enhanced to perform more robust splitting.
See Evaluation of 2D Spots detection.
Shape modelA model for spots based on signal level contours can be built to extract more information from spot valuable for building syntetic images from spot data.
MaintenanceDuring this stage the current system will be mantained and enhanced.
Dye detectionCurrent Dye detection support Comassie Blue, Silver and GrayScale. It is planned to implement a trainable Dye detector and a tutorial on how to train the detector for registration of new dyes.
Axis detectionDetection of axis (I&PM) based on spots found in image.

Development Plan

For the development of this stage, the gel images that we have are enough for development; but more gel images will be of great help to consider new pathologies.
A solution to reach each goal will be developed and frecuent releases will be published for testing.

Conclusions

How much effort - resources?

One person (myself) during three months (3 months) will be required for the development.

How long must we wait?

I have all the required resources to start working.

Cost of development.

The cost related to the tasks defined in this document, will be of 2000 euros.

What will be included with the software?

Contact information

Alejandro F. Reimondo
eMail address aleReimondo en smalltalking.net
MSN address aleReimondo@hotmail.com
(warning: do not use this address for email)