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mesoSPIMmat

This repository contains tools for handling mesoSPIM data in MATLAB.

Contents

  • Tools for handling raw data files: mesotools.rawReader, mesotools.rawWriter, mesotools.metaDataReader
  • bare-bones de-wobbler for parasitic motion of z-stage: wobbleRemover

De-wobbler

Some of the original mesoSPIMs have x and z-drives which have a small, periodic side-to-side "wobble" as they move. This originates from play in the lead-screw and should have a period of 500 microns and amplitude of about 15 to 30 microns. The exact amplitude and phase will vary from system to system but should be consistent within a system from run to run. This tool models the error as a sine wave and cancels it out. It has so far been tested only for z motion, where the problem is probably more of an issue.

wobbleRemove is a MATLAB class that allows the user to interactively remove much of the wobble artifact using a simple GUI. The tool is currently a very early version and hardly tested. To use:

% Load the file as follows:
>> W = wobbleRemove('MyFile.raw');

% You can also load the file separately then feed it to the tool (recommended)
>> data = mesotools.rawReader('MyFile.raw'); 
>> W = wobbleRemove(data);

You will now see a view showing the original image on the left and the corrected image on the right. The sine wave representing the wobble is overlaid on the right image. You can choose a different plane to view by changing the value of the slicePlane property:

% To view slice 300
>> W.slicePlane=300;

You can alter amplitude, phase, or wavelength with the sliders in the secondary window or by modifying the following fields:

W.amplitude  % Currently in pixels (see below)
W.phase      % With respect to z=0
W.wavelength % Likely shouldn't need much tweaking

When you're happy with the effect, you should apply the correction to the whole stack then save the data:

>> W.correctStack % Applies the correction
>> W.saveData % Creates a new file with "_DEWOBBLE" appended to the name
% OR
>> W.saveData(true) % Over-write original (DANGEROUS!)

Running the tool with no input arguments will bring up a basic demo dataset.

Results

The following two images were obtained from the same stack and illustrate the sort of improvement you can expect after about 5 minutes of tweaking. There is still room for improvement, but it's vastly better than the raw data. The lightsheet was made very thick by adding a large offset to the ETL amplitude in order to bring out the effect of wobble from the Z stage (since it makes the same structure visible over a large number of z-planes).

Further work is likely needed to come up with ways to derive the parameters automatically, to assist in the search, or to constrain them substantially.

Known issues

  • The number of microns per pixel is hard-coded as "1" and so the amplitude of the wobble line is in pixels not microns

License

This code is released under GPL v3. Please see attached LICENSE.txt for details if you plan to distribute the code yourself.