#2 spectral imaging support

[Dan White]

The olympus FV1000 and zeiss meta microscope and possilbe others can take spectral images.
This means it collects an image for each fluorescence emission (or possibly excitation) wavelength you set in the microscope software.
So you end up with a series of images of the same plane (or also a set of z stacks) each at a different wavelength. Our .oif reader and lsm reader doesnt know about this, so these data files will fail to load, and further BXD has no way of handling these spectral data sets.

I suggest starting with spectral .oif files, i can get a sample data set from sanna here.
The header file shouls give info for what the excitation wavelength band is, and what he excitation band is for each image (or stack).
We should then colour each image (or stack) with the RGB value corresponding to the median/middle emission wavelength of that image or stack. Alternatively they could jsut all be greyscale.

In this case then we need a new slider for the wavelength dimension, or have a new sub level in the file tree, where each image or stack is repersented by a file tree item.

once we can read and browse spectral images, we can then implement a new task module for linear un mixing, the algorithms for which are published, and explained by timo zimmermans chapter in the book Cell imaging edited by D. Stephens, published by Scion.

there is an imagej plugin for this, look for spectral unmixing

these jobs are for after the next public beta release of course...