Z-drift correction

With the Huygens Software, a Z-drift correction for 3D Time Series is avaliable. A more complete separate tool is also available (see Object Stabilizer).

The basic corrector runs in Huygens Essential after Doing Deconvolution, and is intended to compensate for movements along the microscope axis due to thermal or other instabilities of the microscope. It operates only on 3D Time Series. In case of a Multi Channel image, the corrector can survey all channels and determine the mean z position of the channels, or it can take one channel as set by the reference channel parameter.

Inside a limited area of the image, the filtered coordinates of the centers of mass of the different time frames will be aligned.

The software carries out the following steps:

1. It determines the object's Z-position for each time frame.
2. It filters these Z-positions using a user-selectable filter.
3. It shifts each frame along Z to align all the filtered positions.

In case of a Multi Channel image, the corrector can survey all channels and determine the mean z position of the channels, or it can take 'One channel' as set by the Reference channel.

After determining the z positions per frame, the z-positions can be filtered with a Median, Gaussian or Kuwahara filter of variable width. When the drift is gradual, a Gaussian filter is probably best. In case of a drift with sudden reversals or outliers a Median filter is best. In case the z positions show sudden jumps, we recommend the edge preserving Kuwahara filter.

This drift correction is done taking some risks, because the drift you correct might be a real movement of your specimen that you may want to track! But this is not usual along the Z direction.

See Time Series Z-drift Imp Faq.