LsmCut v1.0

What are Lsm files and LsmCut?

Lsm files are used by Zeiss microscopes to store acquired data. Lsm files are specialized TIFF files. Each of them may be simple and contains one single 2D image with one color (wavelength), or it can be extremely complicated and contains all images of a multi-color 4D movie.

LsmCut is a software which opens 3D Lsm files [stacks of 2D (X-Y) images] and provides user-friendly ways to do some basic data processing, e.g. X-Z and Y-Z vertical sectioning, creating maximum projection of the stack, channel mixing, and contrast adjustment.

How to use LsmCut?

The interface of LsmCut is straightforward. On the left of the window are the X-Y, X-Z and Y-Z views. There are a vertical line (X) and a horizontal line (Y) on the X-Y view that indicate the position of the Y-Z and X-Z slices. User can use the mouse (or CTRL-arrow keys) to move the lines. Likewise, User can also use the mouse (or PgUp/PgDn) to change the focal plane (Z) shown in the X-Y view. The precise positions in numbers are shown below the Y-Z view.


Tuesday, May 26, 2009

Monday, May 11, 2009

Something experimental

I am doing in vitro actin gliding assay and I find that data analysis is a lot of work. As a programmer, the first thing that comes to my mind is 'can the computer do it for me'? Apparently there is no existing software that does it, so, I roll the sleeves up and try it......

The original movie. The quality of movie is terrible because it is converted to GIF, a format that supports only 256 colors.

Find the filaments. It is not that hard to find filaments in one particular frame; identifying the same filament in two frames is another story.

Remove the background. This is easy.

Vectorization. Very difficult.

Bottom line: If you just want to collect enough filaments and analyze, it is doable. If you want to analyze all the filaments, it is almost impossible.

The code that I have written so far is experimental. For a usable software, it may take a long long time. Lsmcut, however, will have a minor update in two weeks.

Another example:

Tuesday, January 20, 2009

Please post your comments/suggestions here

I don't want to make LsmCut heavyweight, but if you have any idea to improve it, please difinitely let me know.