Create a new data processing workflow

The starting point of the workflow are the raw images. They are represented by a node named RawData. To apply a treatment to these images, you need to create a new node by right-clicking on RawData and selecting New Node.
A new node will appear on the screen. At the moment there is no treatment associated with this node. To add one, double click on it or right click and select Edit Node.
Note: For better ergonomics, users can right-click in the area and select Sort Nodes. This option will organize all nodes to make them easily visible. Nodes can also be moved by dragging and dropping.
In the current window, the Type drop-down menu allows you to select the treatment to be applied from the list of available algorithms (stitching, shading correction, maximum projection, background subtraction, etc.). The Temp. Data check-box can be unchecked if you don't want to save this step to disk. This can be useful to reduce the duration and the total size of the data on the computer/server.

The list of all applicable processes is detailed in the following table.


NO_PROCESSOR	No effect.
SIMPLE_TILING	Position each image at its theoretical position on a global tiling.
STITCH_TILING	Stitch adjacent images of a tiling, taking into account the overlap (requires SIMPLE_TILING before).
STANDARD_DEVIATION_ON_FLY	Calculates the standard deviation of the intensity pixel by pixel of an image stack.
SHADING_CORRECTION	Removes unwanted signals from the image (misalignment, dust in the optical system, ...) Given an image of the background, the following calculation is made for each pixel: (current intensity of the pixel / initial intensity of the pixel on the background) x average intensity of the background.
FILTER	Noise reduction by removing anomalous pixels from an image (despeckle). For each pixel, the intensity values of the surrounding pixels (according to a radius value) are recovered. It is then possible to apply a median or average filter to each pixel from these values. The pixels with an intensity value lower than this calculated value are then ignored (value equal to 0) thanks to a median or average filter (the median filter is recommended).
TIME_MAX	Keep the maximum value for each pixel of a stack from the “Time” dimension.
FOCUS_MAX	Keep the maximum value for each pixel of a stack from the “Z-stack” dimension.
TIME_AVERAGE	Keep the average value for each pixel of a stack from the "Time" dimension.
FOCUS_AVERAGE	Keep the average value for each pixel of a stack from the "Z-stack" dimension.
CHANNEL_MULTICOLOR	Merge images from different channels. The maximum intensity values for each pixel are retrieved and a blend of LUTs is performed.
SUBTRACT_BACKGROUND	Removes background from an image to improve contrast.
CHANNEL_RATIO	Rationalize the intensity of a single pixel using several different channels. The "SUBSTRACT_BACKGROUND" is directly present in "CHANNEL_RATIO" to optimize the output.
MULTI_CHANNEL_MERGE	Merges channels. Mainly used for SPIM with two excitation beams.

Tip: All these elements can be performed after the acquisition or in real-time. Data will be actualized and implemented in the final output during the acquisition.