FileProcessed

Raw locations from Spot tracking (spot trajectories in time) contain the following information:

1. Name/date of the imaged embryo (embryoName)
2. Genotype of the embryo (transgeneGenotype)
3. The developmental time in nc14 of the first frame in trajectoryInfo (devTime)
4. Time at which the first z-slice of each frame is taken (acquisitionTimeInfo)
5. Stage z-position for each frame during imaging (zPositionAdjust).
6. Information of raw spot locations in each nucleus (trajectoryInfo)
   1. XY positions of the nuclear centers (nucCenterXY)
   2. Which stripe the nucleus belongs to (stripeInfo)
   3. XYZ positions and the intensity of the identified red spots (redSpotXYZI)
   4. XYZ positions and the intensity of the identified green spots (greenSpotXYZI)
   5. XYZ positions and the intensity of the identified blue spots (blueSpotXYZI)
   6. Background intensities for each channel (backgroundRGB)

Notes:

1. Raw z-positions need to be adjusted using zPostionAdjust in order to get displacement in the axial dimension,
2. All positions are in pixels. XY pixel size: 107.2 nm; Z pixel size: 335.7 nm.
3. Background intensities are from the spots tracked from the re-tracking step (see Methods, step III of Spot Tracking). Usually, it's the second brightest spot candidate in the nuclei where a 'real spot' is flagged, or the brightest spot candidate in the nuclei where no 'real spot' is tracked.
4. Correction for chromatic aberration is needed in order to get distance between spots of different colors.