ess.imaging.workflow.YmirImageNormalizationWorkflow

ess.imaging.workflow.YmirImageNormalizationWorkflow()

Ymir histogram mode imaging normalization workflow.

Return type:

Pipeline

Default Normalization Formula

\[NormalizedSample_{i} = SampleImageStacks_{i} / BackgroundImage * ScaleFactor\]

\[ScaleFactor = AverageBackgroundPixelCounts / AverageSamplePixelCounts\]

\[ \begin{align}\begin{aligned}SampleImageStacks_{i} = Sample_{i} - mean(DarkCurrent, dim=\text{'time'})\\\text{where } i \text{ is an index of an image.}\\\text{Pixel values less than sample_threshold}\\\text{ are replaced with sample_threshold}.\end{aligned}\end{align} \]

\[ \begin{align}\begin{aligned}BackgroundImage = mean(OpenBeam, dim=\text{'time'}) - mean(DarkCurrent, dim=\text{'time'})\\\text{Pixel values less than } \text{background_threshold}\\\text{ are replaced with } \text{background_threshold}.\end{aligned}\end{align} \]