Changelog

[2.2.1.0] - 2025-09-19

The "filter wheel check" script enables testing of response time of filter wheel during actuation protocols

In TimeLapseController, continue_from_pause now returns a message including the time elapsed for sending the JSON command.

The "fuse views" script:
Enables correction of offsets between views along XYZ.
Saves the results for the switching plane and the offsets correction. The offsets in Z and XY correspond to the location of the peaks (along Z and XY respectively) of the correlation coefficient plots.
Match the images (e.g., the XY offsets and maximum-intensity projections along Z) from the other settings of the same position and save them in the corresponding folders.
In "support functions", added functions to generate projections, filtered arrays, edges of thresholded arrays, centers of mass, and interpolated arrays.
The "object tracking" script allows to set a maximum allowed displacement between time-points for the 3 axes. This is useful when the displacement of the tracked target between time-points is large.
The "position centering" script enables centering of positions. The features are the same as for the object tracking, but here the user chooses a range and a step size for the stack that will be acquired to center the positions.
The "Lightsheet alignment (LS1 Live only)" script supports the alignment features originally present for the LS1 Live microscope. Images with varying Translation Z values are recorded, and the best alignment for each illumination is the one corresponding to the highest image sharpness.

The "object tracking" and "position centering" scripts use common functions for calculating projections, filtered arrays and centers of mass.

In the camera class, added methods to get/set the storage settings, the camera settings, and the view to display.
In all classes, added types of input and output variables.
In the filter wheel class, added method to move to a specific position, and added the property to force the movement.
In the microscope device class, added management of filter wheels.

In the filter wheel class, returned the response time when asking to move to a defined position.

In the "Align and center views" operation of "Microscope alignment", added two gray bands to indicate the tolerance expected with temperature fluctuations over time.
In "Fuse views":
added saving of the fusion results (a figure for each position/time-point and a common report with all positions and time-points) in a folder called "Fusion results".
modified plots to display: the sharpness of both views per each plane; the cumulative difference between the sharpness of the views (i.e. the integral of the difference between sharpness of View 2 and sharpness of View 1); the applied threshold for the detection of the peak of the cumulative difference; the switching plane detected as the peak of the cumulative difference.
added management of copying files from original folders.
In "Service tools", added operation to check the response time of a filter wheel.
In "Object tracking", added management of images containing no stack by raising an error, skipping the image analysis, and continue to next position/time-point.

In "Service tools", operations to align the beam axis and the scan axis were separated.
In "Fuse views", the name of the folder created by the module also contains the name of the settings used for the fusion. This enables the user to run multiple fusions in parallel for the same experiment folder with different settings.
In "Object tracking", changed the default value for the settings to "Settings 1".

In "Object tracking":
The position is updated only if the new coordinates do not exceed the stage range.
The center of the detected object is calculated after subtracting the threshold to the thresholded projection, in order to remove the bias coming from the background.

Added management of window closing not to rise an error when closing the window while an operation is still running.