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[Draft] 2D-Electrophoresis Prototype
Buenos Aires, October/2003.
Alejandro F. Reimondo
The work done to detect bands and lanes in 1D-Electrophoresis images was very important to implement signal detection on gel images considering color and intensity.
Now, we can start the development of 2D-Images support also considering color and properties related with two dimensional difusion.
Goals on 2D-Prototype
- Must consider color information
- The prototype will process color and grayscale images.
- Standard image support: 8 bits per pixel and 32 bits per pixel images will be supported in JPEG, BMP and TIFF format.
- Must be as automatic as posible (avoid human interaction or reduce it to easy assistance).
- Must produce standard output containing:
- The location of the center of the spot (x,y)
- The volume of the spot (when applicable, and computed from pixel values)
- The format must be simple and adapted to be read easilly by the Fuzzy Objects framework that will be used for spot registration. (text and worksheet format will be supported).
- The major work will be done on single spot detection
- merged and malformed spots will not be considered in this stage.
- detection robustness may be conditioned by the effort invested in this stage.
- basic background removal will be implemented.
- basic dust detection and removal will be considered on color images.
I plan to reach an usable/working prototype on 2D in a month of work.
The development of a good prototype is directly related with the amount of samples to work with, so it is VERY important to have images of 2D-Gels (real milk gels) to reach an aceptable solution in short time.
What will we have?
We will have a working prototype for:
- the other team members of the milk project start working with 2D spot information.
- do presentations of the milk project showing some results on gel images.
How much effort - resources?
One person (myself) during one month (30days) will be required for the development.
How long must we wait?
I have all the required resources to start working (we can start NOW).
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?
- Runtime executables and settings.
- A running system and all the support to run eficiently in Lab machines.
- Full source code.
- Documentation of implemented techniques.
- Swiki contents: all the history of the project from the very first day.
Alejandro F. Reimondo