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2DE Framework tour


The current implementation of 2DE spots detection includes:
  1. Image preparation (dye & sample considerations).
  2. Global Background detection.
  3. Shashimi of signal according to gray level.
  4. Dump of spots in text file (File/Save option menú).

Image preparation

Image is managed without any modification to detect dye.
Currently we have implemented grayScale, CoomassieBrilliantBlue, and SilverNitrate detectors, but the framework can handle any dye in the future without great effort.
A NiceToHave(NTH) enhacement is to build a color inference detector to manage future one-color detectors without programming (user guided dye detector).

The image is not cropped nor rotated, but axes can be set in the image to define coordinates.

Background detection


Currently a global background color is considered.

Shashimi stage.


The image is cutted in slices according to signal to build contours.
Contous are used to build signal (intensity) pryramids.
The growing of pyramids is analyzed to control the "grown" of spots and infer where they end and fuse each other.

Currently when two (or more) spots fuse each other, the detection process is terminated and the result/shape of fusion is NOT considered, so fused spots area are excluded from detection. We must continue working to complete the detection of fused spots.

Dump of spots


Spot properties are dumped in a simple text file as usual.
Center of spots are dump using the axis coordinates (if enabled and defined).

Future Enhacements and ToDo list

Whell known patologies:
Uploaded Image: ToDo1.jpgDifuse spots: a Global background can hide difuse spots and they will not be detected. A configuration parameter has been added to manage this situaction.

Mixed & fused spots: Shape analysis of contours can help to manage (reject and split) malformed spots. Currently no effort has been done to perform shape analysis.

Uploaded Image: ToDo2.jpgShape of the contours are not analyzed. In the future a profile of non-eliptical contours can be analyzed to infer saturated spots and manage multiple spot signals.
Uploaded Image: ToDo3.jpgSize of spots are considered.
Salt & pepper noise are currently managed properly.