Pipeline operations layout

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.

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.

Channel

Sets the analysis target channel.

Diameter

Sets the reference objects diameter (max).
Note: Object diameter feature can be measured directly from the dataset with the Measurements tool.

Probability
threshold

Sets the probability threshold coefficient.
Note: You can use the Picker tool to pick a probability from the preview layer directly.

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.

Note: You can use the Calculator tool, to compute the split sensitivity.

Channel

Sets the processing and analysis target channels.

Cell body

Sets the output of another operation as an input. It is recommended to select the Output of the Blob Finder operation as input.

Method

Sets the method for tracing neurons. Each has a set of settings which need to be properly adjusted to get the best result.

–

Threshold-based Reconstructor

This method uses a threshold to separate the foreground from the background. The foreground is searched for connected pixels. These connected pixels are formed into paths and only paths that form a neuron skeleton structure will be kept and used to create a complete trace.

–

Probabilistic Reconstructor

This method calculates the local tubularity of the image data. This tubularity map is searched for seed points. Starting from seed points, using a probability function (Monte-Carlo), trace parts are detected. These trace parts are then merge together to create the complete trace.

Threshold

Sets the threshold values accordingly to the image dynamic range.
Note: You can use the Picker or Calculator to determine the value.

Keep only neurites connected to a cell body

Sets that all traces that are not connected to a cell body should be filtered out.

Min. terminal section length

Sets the minimum length of a trace's terminal sections. Any terminal section with a length smaller than this value will be filtered out.