Image processing pipelines in Image Analyst MKII
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Subtract background and stabilize

Parameters:
Name # Type Description
Background Level (percentile) 1 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 2 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) 3 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 stabilizes the time lapse (registers frames in time) and subtracts background. 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 single-channel recordings, before single-cell analysis. Applicable to Ca2+-imaging (e.g. Fluo-3, GCaMP), reactive oxygen species imaging (e.g. DCFDA), GFP-based sensor imaging.