Changelog

[3.0.1] - 2026-04-10

Software

Fixed

• Fix decreasing camera offset not updating image size.

PyMCS

GUI

Fixed

• Fix wrong encoding of log files (was crashing when executing object-tracking script).

Scripts

Fixed

• In microscope alignment and calibration, camera offsets are reset when user stops the script.
• In microscope alignment, a property is verified not to be null when printing it on the status window.

[3.0.0] - 2026-03-12

Software

Added

• During beam scanning, the laser is triggered ON (respectively, OFF) with a delay to accommodate for the acceleration (respectively, deceleration) of the scanners at the beginning (respectively, end) of the scan. This mitigates the shift and the intensity peak at the extremities of the scanned region for both the tunings of the scanners.
  
• Add wizard to exchange objective blocks.
• Add immersion media selection which affects the magnification and objective alignment.
• Improve objective alignment:
• Add menu to update the objective alignment associated with the current immersion medium from the current illumination alignment.
• Display objective alignment associated with current immersion medium in the illumination module tab.
• Add menu in service mode to save objective alignment as factory settings.
• Improve base offsets calculation in service mode for illumination module and photomanipulation:
• Add arrow buttons to directly edit base offsets.
• Add menu to display a popup that shows the base offsets.
• Add menu to save the base offsets.
• Add menu to save photomanipulation offsets.
• Add option to acquire full field of view in exposure settings (will automatically adjust based on magnification).
• Add uninstaller.
• Auto-import settings from previous versions.
• Integrate PyMCS inside MCS (no separate installation required).
• Add compression with Zstandard for OME-TIFF files.
• Add position-specific Z-Stacks where the number of planes is derived from position's range Z.
• Add support for pyramids (writing/reading) allowing display of full mosaic in image viewer.
• Add support for Leica K8 Camera.
• Add about window with software information.

Changed

• Directory and file name patterns are no longer options of storage.
• Maximum intensity projection is now stored inside optional data folder ("XXX_Optional/MaxZ").
• All settings profiles are now acquired for a tile before proceeding to the next one.
• Pause after position occurs after all position-related tasks (including photomanipulation) are completed.
• Increase no response timeout of Hamamatsu camera driver from 5s to 20s.
• Application is now installed in program files directory and data are stored in program data directory.
• Update SmarAct library to version 1.5.16.0.
• Improve support for filter wheels controlled via serial communication by allowing multiple connections on the same COM port.
• JSON commands are no longer accepted if client is not authenticated.
• Improve robustness of filter wheel serial driver.
• Acquire tiles in snake order (zig-zag) to minimize stage movements.
• Use maximum stage speed for block exchange.
• New exposure settings have full field of view by default.
• Remove photomanipulation auto-trigger option in acquisition settings (trigger if photomanipulation defined for a position and time point).

Removed

• Remove "Calculate base offsets" menu from illumination module and photomanipulation.

Fixed

• Fix crash when opening virtual hand controller window.
• Fix crash when starting application without photomanipulation component.
• Fix missing error reporting in the time-lapse controller initialization.
• Fix error when DeviceSettings is undefined in acquisition settings.
• Fix position alignment for snap and live acquisition.
• Check signature of Python interpreter executable to ensure security.
• Fix invalid Y-coordinate when marking positions for range XY.
• Fix settings conversion issue when importing settings from previous versions.
• Fix crash when receiving invalid JSON command.
• Fix invalid creation of markers for range XY.
• Fix application not closing properly when closed during startup.
• Fix premature stopping of stage movement.

JSON API

Added

• Add Authenticate command to authenticate client before sending other commands.
• Add GetIlluminationList command to illumination module.
• Add ExposureTime, ScanRange, ScanFullFOV, Views and SettableDeviceSettings to Snap command.
• Add new ObjectiveBlock component with the following commands:
• GetObjectiveBlockInfo
• SetShading
• Add UpdateObjectiveBlockAlignment, GetObjectiveBlockAlignment and SetObjectiveBlockAlignment commands to illumination module.
• Add GetTiltFactors, SetTiltFactors and SaveTiltFactors commands to acquisition controller.
• Add MoveTo command to stage component to move stage to absolute position.
• Add GetCoordinates command to stage component to get current absolute position of stage.
• Add GetSensorInfo command to camera component to get sensor information such size and temperature.

Changed

• Rename GetDeviceList into GetComponentList. Response properties are now ComponentNames and ComponentTypes.
• Rename GetDeviceType into GetComponentType. Argument is now QueryComponentName. Response property is now ComponentType.
• Remove Device suffix from component types.

Removed

• Remove LaserAblateUV command.
• Remove TranslationY from IlluminationSet command of illumination module.
• Remove TranslationY from IlluminationGet and CurrentIlluminationGet responses of illumination module.
• Remove OffsetsInternal parameter from OffsetsBaseGet and OffsetsBaseSet commands of photomanipulation.

Settings

Added

• Add TaskCacheSize in application settings for controlling the maximum size of the task cache system.
• Add BlockExchangePosition in stage component settings.
• Add IsRangeFullFOV in exposure user settings.
• Add CameraName to acquisition controller component settings.
• Add ObjectiveBlockName to acquisition controller, illumination module, camera and time-lapse controller component settings.
• Add DarkOffset and SensorPixelSize to camera component settings.
• Add new objective block component settings.
• Add new objective block objective settings to store objective block properties (objective, magnification and numerical aperture for illumination and detection objectives).
• Add new immersion medium user settings to store immersion medium properties (name, refractive index, shading correction factor).
• Add new illumination objective user settings to store objective alignment for each pair of illumination branch and immersion medium.

Changed

• Merge ImagePositionX, ImagePositionY, ImagingPositionZ into ImagePosition in stage component settings.
• Merge LoadPositionX, LoadPositionY, LoadPositionZ into LoadPosition in stage component settings.
• Move Objective, Magnification and NumericAperture from camera objective settings to objective block objective settings as Objective, DetectionMagnification and DetectionNumericalAperture.
• Rename View1and2 into View1And2 in Views of acquisition settings.
• Rename OffsetsBase into BaseOffsets in illumination module component settings.
• Rename OffsetsBaseInternal into InternalBaseOffsets and OffsetsBaseExternal into ExternalBaseOffsets in photomanipulation component settings.
• Move PositionXLimit, PositionYLimit, PositionZLimit and StageDirection from stage component settings to stage objective settings.

Removed

• Remove MagFactors from camera component settings.
• Remove MagFactor from camera user settings.
• Remove illumination module objective settings (now in illumination objective user settings).
• Remove ShowTranslationY from illumination module component settings.
• Remove TranslationY from illumination module user settings.
• Remove the following properties from acquisition controller component settings:
• MicroscopeModel
• Illumin1Scanner1AOChannel
• Illumin1Scanner2AOChannel
• Illumin2Scanner1AOChannel
• Illumin2Scanner2AOChannel
• Illumin1Scanner1Offset
• Illumin1Scanner1Factor
• Illumin1Scanner1Disabled
• Illumin1Scanner2Offset
• Illumin1Scanner2Factor
• Illumin1ScannerRelation
• Illumin2Scanner1Offset
• Illumin2Scanner1Factor
• Illumin2Scanner1Disabled
• Illumin2Scanner2Offset
• Illumin2Scanner2Factor
• Illumin2ScannerRelation
• AblationLaserUVDOChannel
• Remove ExternalBaseOffsets from photomanipulation component settings.
• Remove PyMCSPath from PyMCS launcher component settings.
• Remove Enabled from photomanipulation in acquisition settings, photomanipulation is enabled if defined for a position and time point.

PyMCS

Library

Added

• In the time-lapse controller class, the snap method enables setting of additional properties
• Add method to move the stage to a defined XYZ position.
• Add method to get the size of the camera sensor.

Changed

• Microscope devices are replaced by microscope components.

Advanced modules

Added

• The "objective block alignment" script enables alignment of an objective block. It aligns both rotations and translation, and save the values in the corresponding settings. These values are refractive-index dependent.
  
• The "scan plane alignment" script enables alignment of the scan plane of the beams. It also enables the measurement of the applied correction and the measurement of the angle between the focal planes of the 2 views. This values are refractive-index independent.
  
• The "shading correction" script enables correction of the shading effect (also known as vignetting) over the FOV.
  
• The "align camera rotation" operation of the "microscope calibration" script enables alignment of the camera rotation relative to the microscope base.
  
• Add script implementing the Moisan algorithms [J. Math. Imag. Vision 39(2), 161-179, doi:10.1007/s10851-010-0227-1] to calculate the smooth and periodic components of an image, and the corresponding Fourier transform with reduced edge artifacts.
• In lightsheet alignment, add management of microscope components.
• In filter wheel check, add the option to actuate illumination filter wheel.

Changed

• "Service tools" are replaced by "Microscope calibration".
• In "Microscope alignment" the automated TranslZ alignment is moved after the manual TranslY to prevent the manual alignment from defocusing the beams.
• Subtract background for camera rotation alignment in microscope calibration.
• In microscope calibration, display difference with the target angle when measuring the center of the illumination aperture, and handle the situation when only one view is used when aligning camera rotation.
• In the alignment scripts, use sensor size, image size and offset to determine if the sensor has been cropped.
• Rename "Lightsheet alignment" into "Lightsheet alignment (on sample)".

Removed

• Remove "Fused views" advanced module, should use post-processing software now.

GUI

Added

• When started without terminal, all messages are logged on files.

Changed

• GUI expect full path of script rather than just name.
• Can be launched without terminal (with pythonw.exe).

[2.2.1.0] - 2025-08-14

Software

Added

• The edition of settings will not affect the current time point execution.
• Add warning message when changing settings during time-lapse.
  
• Prevent the edition of some settings while time-lapse is running.
• Add "Never" option when acquiring a channel every nth time points to disable it while the time-lapse is running.
• User settings may be marked as required (from JSON file), preventing renaming and deletion at all time.
• Add new "Range XY" tab to define the range of positions in the XY plane.
  
• Acquire multiple tiles for each position based on range XY when defined. Tiles can be visualized and navigated using a minimap in the image viewer.
  

Changed

• Automatically disconnect when an unrecoverable error occurs in a device.
• Improve speed of aborting time-lapse (almost instantaneous).

Settings

Added

• Add MinTileOverlap in stage component settings.

PyMCS

Advanced modules

Added

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

Changed

• In "service tools", remove operation that measures response time of a device.

[2.2.0.2] - 2025-08-06

Software

Fixed

• Fix TIFF writing when transitioning to BigTIFF format (no random pixels at the top of plane close to 405).

[2.2.0.1] - 2025-07-07

Software

Fixed

• Fix overlay not overlapping properly in image viewer.

[2.2.0.0] - 2025-07-01

Software

Added

• Add interactable histogram on top of image viewer.
• Displayable from context menu.
• Y axis can be displayed in log scale.
• Clicking will adjust max threshold.
  
• Add retrospective image browsing, can look at old time points, settings or positions.
• Add buttons to follow latest plane and time point imaged.
  
• Add toolbar with buttons for histogram and maximum intensity projection (when available).
  
• Add delay and duration of time point.
• Don't stop acquisition if a delay is detected (shows warning).
  
• Show error if acquisition completes with a delay.
  
• Show duration of last time point.
  
• Display time stamp in image viewer and store it in ome metadata.
• Add coordinates in ome metadata.
• Documentation of the JSON commands API.
• Documentation of the JSON settings.
• Automatic settings conversion from previous version at application startup and settings import. Compatibility starts from version 2.0.0.5
• Add objective block selection at startup, moved all objective block settings in a dedicated folder.
  
• Add saturation color lookup table (white with red when value is maximum: 65535).
  
• Add the virtual hand controller window that can move the stage by clicking on arrows buttons (also work with keyboard). The step size of the move can be defined.
  
• Allow to define range Z of positions in a dedicated editor tab where it is possible to mark the edges based on stage location. The center Z will always be in the middle of the range.
  => =>
• Allow photomanipulation at multiple positions and multiple time points.
• Add menu option to reset learned flow of CO2 and O2 concentration in environment control. There is also a warning when starting the flow regulation if the flow is unexpectedly high.
• Add service mode when pressing Shift key at software startup.
• Add a menu item in service mode that allows to bypass the min/max validation of illumination module settings.
• Add company name, software name and version in the image metadata.
• Add correction factor for translation-rotation coupling in ACQ_Component of Microscope settings. This factor corrects for the additional rotation induced by scanner 2 when translating the beam along X, since scanner 2 is not at the focal plane of the scan lens. The red and green lightsheets in the picture are the uncorrected and the corrected one, respectively.
  
• Add correction factors for scan plane tilts in ACQ_Objective of Objective settings. These factors enables alignment of the scan planes of each illumination with the imaging planes of the cameras. The pictures show the uncorrected (i.e. tilted) and corrected (i.e. horizontal) planes. The fact that the imaging planes are curved is due to the field curvature of the detection objectives.
  
  

Changed

• When autoscale is enabled, display which scaling is used instead of manual scaling values.
• Change position selection in acquisition settings to dropdown with checkboxes.
  
• Change path selection input to file dialog.
  
• Change how EULA are displayed. The EULA is now displayed in a separate window and the user must accept it to continue.
  

Fixed

• Photomanipulation images are now valid ome.tiff (openable with ImageJ).
• Maximum projection images are now valid ome.tiff (openable with ImageJ).
• Fix crash when PyMCS is already opened.
• Fix missing colors in channel presets.

Settings

Added

• Add Version to application and user settings.
• Add PanelLocation in filter wheel and illumination module component settings.
• Add new component settings file for time lapse controller, JSON command server, PyMCS launcher and image viewer.
• Photomanipulation component settings:
• Add StageXYZName.
• Acquisition controller component settings:
• Add PhotomanName.
• Camera component settings:
• Add StageXYZName.
• Add FlowExcessThreshold to environment control PID settings (PID_EIntegrals<gas>.json).
• Add LaserExternal to photomanipulation component settings.
• Add Scanner2To3Factor to acquisition controller component settings.
  This factor is used to correct for the additional rotation induced by scanner 2 when translating the beam along X, since scanner 2 is not at the focal plane of the scan lens.
• Add Illumin1TiltFactor and Illumin2TiltFactor to acquisition controller objective settings. These factors enables alignment of the scan planes of each illumination with the imaging planes of the cameras.
• Add residual offsets in illumination module objective settings to compensate for residual objective block misalignment.

Changed

• Move device/component name from MicroscopeDevices.json into MicroscopeSettings.json under Components.
• Move device type and label from MicroscopeDevices.json into component settings file.
• Convert device settings into components settings:
• Rename XXX_Device.json into XXX_Component.json.
• Rename DeviceType into ComponentType.
• Rename DeviceLabel into ComponentLabel.
• Converted user settings list into object (to store additional properties, e.g. Version).
• Acquisition settings:
• Merge TimeIntervalMin and TimeIntervalSec into TimeInterval.
• Rename Settings into SettingsProfiles.
• Rename ZStackName into ZStack.
• Rename IlluminationSetting into Illumination.
• Rename ExposureSetting into Exposure.
• Rename IlluminationFilterSetting into IlluminationFilter.
• Convert Positions of settings profiles to be a list of positions name.
• Convert Positions of photomanipulation to be a list of positions name.
• Rename TimePoint of photomanipulation into TimePoints and convert to be a list of time points.
• All component settings:
• Rename StageXYZDeviceName into StageXYZName.
• Rename Illumin1DeviceName into IlluminModule1Name.
• Rename Illumin2DeviceName into IlluminModule2Name.
• Application settings:
• Move PyMCSPath into PyMCS launcher component settings.
• Move PythonInterpreter into PyMCS launcher component settings.
• Move objective settings into a Objective/ folder.

Removed

• Delete MicroscopeDevices.json.
• Acquisition settings:
• Remove ZStackEnabled, no ZStack means disabled.
• Remove old image formats from camera storage settings (TIFF Stack and TIFF Image).
• Remove unused ADLS1_Module.json and ADLS2_Module.json files.
• Remove unused photomanipulation driver settings file.
• Remove Overlays from camera settings.

PyMCS

Library

Changed

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

Advanced modules

Added

• 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.
  

Changed

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

[2.1.0.1] - 2025-02-06

Software

Fixed

• Photomanipulation tab was displayed when it was unavailable.

[2.1.0.0] - 2025-01-06

Software

Added

• Add scale bar.
  
• Add settings summary.
  A user readable text file is available in the experiment folder when an acquisition is performed. This file contains all the settings used in the current acquisition.
• Add End User License Agreement at startup.
• Add notice file for open source libraries.
• Add a menu to calculate scanner base offsets for photomanipulation.

Changed

• Update validation of names to work with file system.
• Improve validation of acquisition settings.
  
• Improve efficiency when moving through planes in image viewer.
• Update logo to Leica's and change icon colors.
  
• Detect compatible PyMCS version based on two first version numbers (Milestone and Major).
• Bypass driver communication in Move commands.
  FilterWheelDevice commands Move and MoveTo skip sending a move command to the driver if filter wheel is already at the correct position.
• Extend MAC6000FilterWheel driver hardware response timeout to 10s.
• Increase range of photomanipulation scanner offset from +-10um to +-20um.

Fixed

• Fix inconsistent numeric validation.
  Some numeric fields compatible with arithmetic computation were not replaced by the result once saved.
  =>
• Fix crash when editing the Z-stack parameters.
• Fix text hidden behind text box icon.
• Fix text box resizing for long text.
• Fix switch of view when moving photomanipulation area in image viewer.
• Fix invalid position computation from image viewer.

JSON API

Added

• Add option to set device to IlluminationSet command of illumination device
• Add option to snap fast to Snap command of time lapse controller to bypass the setting of all settable devices.
• Add a command to set the displayed view from PyMCS: DisplayedViewSet.
• Add Force option to Move commands.
  Add a Force option to FilterWheelDevice commands Move and MoveTo which forces move command to be sent to the driver even if filter wheel is already at the correct position.

Changed

• Rename With into Width for ImageGet response of CameraDevice.

Settings

Added

• Add gas concentration regular expression settings and manual COM port settings.
• Add manual COM port settings to SerialFilterWheel driver.

Removed

• Scanner factors of illumination module are now ignored (set from acquisition controller).

PyMCS

Library

Added

• 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.

Changed

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

Advanced modules

Added

• 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.

Changed

• 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".

Fixed

• 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.

GUI

Added

• Created a mouse-right-click event.

Changed

• Changed to Leica logo and color.
• Increased space for help messages.

Fixed

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