, Use Imaris Bitplane software for 3D automatic tracking
, Open the 3D image sequence on Imaris. Select "spot" command, and generate manual tracking (mouse click+shift) for all time points for a minimum of 4 different anchor points
, Apply the drift correction using
, Check for the quality of the correction in x, y and particularly in z to avoid artefactual wavering. NOTE: If the correction is not satisfactory
, Cell tracking 1. Use "add new spots" command and select "track spots over time" algorithm setting. Go to next step
, NOTE: The choice will depend on the distinction between objects and specificity of the measured signal. In short, automatic tracking on the whole channel is possible only if detected signal is specific to the object of interest. Because both SHG and ECFP are detected by the NDD after the 485 short pass filter, tracking will be more specific and efficient using the ECFP signal recorded by the NDD after the 500/550 bandpass filters. Clustered or dense packed objects will require manual selection of, Apply automatic cell tracking procedure either on the whole channel of interest using "source channel" command. Set objects (i.e., cells) diameter to 10 µm. Go to next step
, Select "quality" filter type, set the threshold to exclude tracking of unspecific objects. Go to next step
, Brownian Algorithm Motion" with accurate parameters of "Max distance" and "Gap size" between two spots. Validate track generation
, Once tracks are automatically calculated, select "track duration" filter type, set the threshold to eliminate tracks shorter than 120 sec
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