ZEISS Knowledge Base

Pipeline operations layout

The following operations are part of the pipeline.

Input ROI

This operation allows to select the region of interest (ROI). ROI defines the dataset sub-volume that will be processed and analyzed by the pipeline.

Parameter		Description
ROI		Sets the processing and analysis target space.
–	Current View	The selected Z plane and the viewer area are processed.
–	Current Plane	The selected Z plane is processed (XY).
–	Current Time Point	The selected time point is processed (XYZ).
–	Current Image Set	The complete dataset (XYZ and time) is processed.
–	Custom	Allows to mix the previous methods. Note: Use the Custom option during the pipeline setting and testing. Set a sub volume (XY, Planes, Time Points, channels) of your dataset on which perform the trial. This will speed up the setting process.
Channels		Sets the processing and analysis target channels. Selecting a single channel, all the operations in the pipeline will be forced to use it.
Scaling		Sets the scaling of the dataset, which reduces it size. The measurements will not be modified by the scaling factor
Crop input data		Sets the limitation of the data used for the calculation to only the cropped selection defined above. If this option is not selected, the entire image set is used for the calculation.

Additional settings for Input ROI expand, when you click in the operation.

Parameter	Description
Bounds	Sets the analysis area edges. The whole XY bounds, the viewing area or a custom space can be applied.
Planes	Sets the analysis planes range. A single plane, a range of planes or the whole stack can be selected.
Time Points	Sets the analysis time points range. A single time pint, a range of time points or the whole movie can be selected.

Detects the cell body starting from the membrane marker.

Parameter		Description
Channels		Sets the processing and analysis target channels.
Min intensity (membrane)		Sets an approximation of a membrane with the lowest intensity. This value is used for the initial thresholding of the image to extract the membrane and thus separate it from the background. This is a very important and guiding value, therefore it needs to be selected carefully.
Split sensitivity		Sets the sensitivity used to split touching objects. Decreasing the Split sensitivity will fuse more objects . Increasing the Split sensitivity will split more objects.
Membrane Maximum		Sets the membrane maximum size. Drop down the list to select the feature
–	Max. diameter	Sets the value as the maximum diameter. Note: You can measure the membrane maximum diameter directly from the dataset with the Measurement tool.
–	Max. area	Sets the value as the maximum area. Note: You can measure the membrane maximum diameter directly from the dataset with the Measurement tool.
–	Max. volume	Sets the value as the maximum volume. Note: You can measure the membrane maximum diameter directly from the dataset with the Measurement tool.

Store the detected segments (tag) in the active dataset.