Pipeline operations layout

ROI

Sets the processing and analysis target space.

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Current View

The selected Z plane and the viewer area are processed.

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Current Plane

The selected Z plane is processed (XY).

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Current Time Point

The selected time point is processed (XYZ).

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Current Image Set

The complete dataset (XYZ and time) is processed.

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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 channel where the cells will be segmented.

Optional channel

Sets a second optional channel (e.g., nuclei channel) to support the segmentation.

Cellpose model

Sets a pre-trained cellpose model from the list of built-in models.

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CP

Sets a model, which is mainly trained on fluorescent cell images .

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CPx

Sets a model, which is trained on wide variety of images.

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Cyto

Sets a cytoplasm model, which is trained on one channel cell images (if the image had a nuclear channel).

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Cyto2

Sets a cytoplasm model, which is trained on two channels cell images (if the image had a nuclear channel).

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Nuclei

Sets a model, which is trained on two-channel images. The first channel is the channel to segment, and the second channel is always set to an array of zeros.

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Load external model

Sets a custom model, which allows you to load and run your trained Cellpose models or any pre-trained Cellpose models not included in the operation.
Note: Refer to the Help (F1) for more information.

Cell diameter

Sets value of the diameter of your cells. Alternatively, use the Measure tool to determine it.

Min area

Sets the reference objects diameter. Select a value to filter out the objects with smaller area, volume, or diameter.

Mask threshold

Sets the cell probability threshold between -6 and +6 to determine what is a cell and what is background.

Mask quality threshold

Sets the maximum allowable errors (mean square error) of the flows for each detected cell. The filter range is between 0 and 1 to exclude masks with lower quality values.

Smooth Cellpose model results

Sets the Gaussian smoothing process, to refine the output, reduce noise and potentially improve the overall performance of your cell detection application.

Normalization percentile

Sets the normalization range. The default values are 1% to 99%, where everything below the lower threshold and everything above the upper threshold is mapped out as outliers.

Note:Increase the range if you have data with big background areas and very little area of actual bright signal