Prepare two-channel time lapse for intensity analysis

Parameters:

Name	#	Type	Description
Channel number #1	1	integer	Channel number associated with the image. Use Edit/Rename to view or change channel number.
Channel number #2	2	integer	Channel number associated with the image. Use Edit/Rename to view or change channel number.
Background Level (Percentile)	3	real	Background is calculated as frame-by-frame median of those pixels that are the darker than this percentile of image histogram for the duration of the entire recording.
Image stabilizer compares to first frame	4	boolean	“Yes” is the fastest way of image stabilization. Turn it off if the image changes a lot during the time lapse, and it is not possible to compare later frames to the first frame any more
Image stabilizer period (frames)	5	integer	1 if comparing to the first frame. Use more frames if not comparing to the first frame and the view field drifts slowly.

Description:

This pipeline corrects for misalignment between channels on the frame-by-frame basis, subtracts background, and stabilizes the time lapse (registers frames in time). To eliminate background the “Median of pixels below percentile of max projection” with the percentile given at “Background level” is used.
Use: generic pre-processing for two-channel recordings, before single-cell analysis. Applicable to Ca2+-imaging (e.g. Fura-2, yellow cameleons), other ratiometric ion probes imaging (e.g. PBFI, SPFI, SNARF-1, BCECF), reactive oxygen species imaging (e.g. HyPer, roGFP), intramolecular FRET sensor imaging, potentiometric probes (TMRM plus FLIPR).

Version history:
V2
Changed caption