softWoRx® 7.2.2 Release Notes
June, 2020

© 2020 Cytiva – All rights reserved.

Introduction

softWoRx version 7.2.2 is a minor release providing brand awareness.

Changes and Additions

· We're now Cytiva!

Known Problems and Workarounds

• Task Builder -> OMX Align Image: When using the Legacy Shift and Rotate method with Apply Z Alignment selected, the Z alignment offsets are applied twice.
• Workaround: Deselect Apply Z Alignment when using this method or use the graphical softWoRx tool Process->Legacy->OMX Image Registration and specify the Shift and Rotate Registration Method which correctly applies the Z alignment.
• DeltaVision Panel File Format: Images collected using the Panel or Plate Scan (with multiple panel sites) capabilities in Resolve3D or AcquireUltra are not compatible with softWoRx versions older than 7.0.0. If these files are stitched on a system running 7.0.0 or later, they may then be used with older software.
• DeltaVision Acquisition: The Fast Acquisition state can interfere with running a time-lapse Plate Scan experiment. If Fast Acquisition is toggled On and the Conventional Time Lapse Fast Acquisition Option is toggled Off, only one time point will be collected.
• Workaround: Toggle Plate Scan Off temporarily (which enables the Fast Acquisition check box), switch Fast Acquisition Off, then switch Plate Scan back On.
• Image Buffer Overwrite: When using the sCMOS camera during a fast acquisition experiment with the Entire Scan shutter mode enabled (the fastest frame rate mode) and using a combination of large image sizes (1k x 1k and larger) and very short time lapse values (< 5 ms), it is possible that the instrument controller may not be able to process the acquired images from the memory buffer fast enough. When this happens, an image on the buffer waiting for download is overwritten with a new image. The new image is then captured as the image for the previous timepoint.
• Workaround: Reduce the frame rate by using longer time lapse values, reducing the image size, or reducing the number of timepoints.
• Image Window (Copy/Paste Scale): If a "copied" set of display scale values exceed the Minimum and/or Maximum values in the image to which the values are "pasted," the scale values will be truncated to fit within the Minimum/Maximum range. 
• Workaround: Manually type the values into the Min/Max/Exp field of the Scale tool belonging to the window that will contain the pasted values.
• Image Window (Save...): If one or more of the channels is toggled Off in the Save tool, incorrect scaling of the output image may result.
• Workaround: Use the Copy Region tool from the main softWoRx menu bar and send the output to a file instead of a window.
• softWoRx: It has been reported that individual user accounts seem to lose permission to run softWoRx. 
• Workaround: A possible workaround is to remove (or rename) the file "user.swrc" in the .softworx_<hostname> subdirectory of the user account's home directory.
• softWoRx: Some older softWoRx versions or 3rd-party analysis tools can have difficulty with the latest softWoRx default data type.
• Workaround: Open the image with softWoRx and choose Save from the File menu of the image window. Choose Details..., and change the Data Type from No Change to 2-byte signed integer. Then, save a new copy of the file.
• Stitch: If you choose a subset of Z sections (from the Details... dialog), Stitch may fail.
• Workaround: Restart softWoRx and try again.
• Save As Movie: Saving a time-lapse image as a Movie when the window is in Montage By Time viewing mode may cause Save As Movie to crash. 
• Workaround: Try choosing the maximum that the image window time slider will go and specify that number for the End time in the Time: Start/End/Increment field of the Save As Movie tool.  Then, select Do It.
• Save As Movie: Using the Movie tool to play the window as a movie while Save As Movie is capturing images can cause the Image window to crash.
• Workaround: Pause all other movie tools prior to pushing Do It for the Save As Movie tool.
• Save As Movie: Attempts to save more than one movie at a time can cause crashes of either the Save As Movie tool or the Image Window that it is using.
• Workaround: Ensure any previous Save As Movie processes have completed before starting a new one.
• Align Image: This tool can be unreliable when it is used on a single-channel image.
• Workaround: There is currently no known workaround for this issue.
• Calibration File: Calibration files are created with the file name extension .dv_cal and may not be viewable in softWoRx by default.
• Workaround: Choose File -> Open from the softWoRx main menu and change the File Types filter from *.dv to *
• Save As Movie: Graphical elements (like Line Profile graphics) are not accurately synchronized with the image data when movie frames are captured.
• Workaround: There is currently no known workaround for this issue.
• Deconvolution: Attempting to run two or more simultaneous multi-processor Deconvolution jobs on a multi-core workstation may occasionally cause severe slowing of all processing on the workstation. 
• Workaround: If this happens, cancel all but one of the jobs and allow it to complete before starting any further jobs.

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Release Notes for Previous Versions

Version 7.2.1

softWoRx version 7.2.1 is a minor release providing increased reliability.

Changes and Additions

Software Defects Fixed:

• Export to IN Carta: The Export to IN Carta tool is now compatible with Acquire Ultra 1.2.0
• Task Builder: The Volume Rendering task now properly applies the chosen rendering method to all channels of the image
• Resolve3D: Experiments containing Reference Images and Panels are now supported
• Image Window: The unsupported Print option has been removed from the File menu

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Version 7.2.0

softWoRx version 7.2.0 is a major release providing improved functionality and increased reliability.

Changes and Additions

Software Environment:

•  softWoRx is now supported on CentOS 5-7. This release is intended to support DeltaVision (including Ultra, Elite, and other legacy systems), and DeltaVision OMX processing.

Desktop Environment:

• "Start Acquire Ultra" and "Stop Acquire Ultra" are  now accessible from icons in the desktop's "Kickoff Application Launcher" menu

Enhancements:

• Task Builder: An option to save results as 4-byte floating-point has been added to the Deconvolution task options. This will appear in both the softWoRx Task Builder and the Post-Acquisition Processing tasks in the Run Experiment page in Resolve3D.

Software Defects Fixed:

• Align Image: The Align Image user interface has been reworked to fix several issues related to specifying input images
• Stitch: The system configuration is updated by the Acquire Ultra installation package to update the stage polarity parameters for DeltaVision Ultra systems
• Export Ultra to IN Carta: A problem with setting the output folder to be the same as the experiment parent folder has been resolved
• OMX Align Image: The tool is more tolerant of small image sizes and better communicates errors when problems arise
• Image Window: An issue that could have caused Image Windows to fail when re-using them have been resolved
• Resolve3D: Post Processing Options dialog box now can be closed without selecting any tasks
• Enhance Contrast: The tool no longer crashes with non-square images

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Version 7.1.0

softWoRx version 7.1.0 is a major release providing improved functionality and increased reliability.

Changes and Additions

Acquisition (AcquireUltra):
AcquireUltra is the fully re-designed acquisition client created to support the DV Ultra microscope system.

Software Environment:

•  softWoRx is now supported on CentOS 7.

Processing and Analysis:

• Added capability to export AcquireUltra plate scan to IN Carta (marked as Beta)
• Added Flat Field Correction of AcquireUltra images

Software Defects Fixed:

• Resolve3D: Panel Experiment canceled during first time point now removes incomplete image file
• Resolve3D: Critical / Kohler setting is now noted in the image log file
• Resolve3D: Now writes the proper "1.0" photosensor value in the log file when Use Photosensor is turned Off
• Resolve3D: Panel experiment with Z sectioning now starts at the correct Z position
• Resolve3D: Deconvolve During Experiment now properly checks the time lapse conditions
• Stitch: Reduction Factor now properly applies to both X and Y axes
• Rotate3D: Crash has been fixed
• AlignImage: No longer crashes when an Image Window number is dragged in to the Input field
• Save: Saving a raw OMX file from an Image Window no longer corrupts the Image Window
• Movie: The movie tool no longer crashes softWoRx when running multiple movies quickly
• Task Builder: OMX Reconstruction now guards against illegal Weiner filter values
• Create Widefield From SI: The tool no longer crashes when the output file name is changed
• OMX Align Image: No longer fails when doing Z alignment step
• OMX Align Image: Z alignment is now done before the XY alignment to improve performance
• OMX Align Image: Z alignment is no longer attempted if the image has less than 2 Z sections
• OMX Align Image: No longer quietly fails with 2048x2048 image files
• OMX Align Image: Processing speed has been improved
• OMX Align Image: No longer fails at certain pixel sizes

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Version 7.0.0

softWoRx version 7.0.0 is a major release providing improved functionality and increased reliability.

Changes and Additions

Software Environment:

• All of the softWoRx software components running on the workstation are 64-bit applications.
• Shared memory sizes may be set much larger (15Gb) due to 64-bit memory addressing.
• The DeltaVision file format has been expanded to include a "Panel" dimension to better accommodate plate scanning and multi-panel acquisition.

Acquisition (Resolve3D):

• Paneling is available for experiments with Z Sectioning, Multiple Channels, Time Lapse, and Point Visiting.
• Time Lapse imaging honors a per-channel Frequency setting for regular channels and Reference Image channels.
• A Multi-Channel Reference Image capability has been added to the Experiment Design.
• Stage View is now moveable and resizable.
• Stage View thumbnails now have a resolution factor that can be specified in Settings.
• Stage View thumbnails can be adjusted for brightness.
• Image Scan Sequence may be specified for Fast or Conventional imaging modes.
• Fields of View in Plate Scan experiments now use the file format's Panel dimension, so separate files for fields are no longer required.

DeltaVision Processing Capabilities:

• The Deconvolution tool has been improved to manage much larger images and provide more rapid convergence for enhanced ratio deconvolution.
• Task Builder Process Chains may now be saved to be opened later.
• Stitching has been added to the Task Builder.

OMX Processing Capabilities:

• A new robust OMX Image Alignment method has been added. Earlier tools are still available in a "Legacy" submenu.
• OMX Image Alignment Calibration plots markers on the input grid image to indicate where usable alignment points are found.

Software Defects Fixed

• DeltaVision Acquisition: Panel experiments may now be created  with one row or one column.
• DeltaVision Acquisition: Deconvolve During Time Lapse experiments can now work along with experiment Post-Processing tasks.
• DeltaVision Acquisition: The Point List now properly updates Z coordinates after running an experiment with UltimateFocus.
• DeltaVision Acquisition: Stage View thumbnails no longer disappear when the lower left hits the left and bottom borders of the view.
• DeltaVision Acquisition: Size requirements for a Plate or Point Visit experiment are calculated correctly and updated during the experiment.
• OMX Image Registration: The aligned image file no longer gets corrupted when Z offsets are set to the same non-zero value.
• OMX Image Registration: Intensity Mean values are now correct for images with Z shifts specified.
• OMX Image Registration: Shift and Rotate method now works properly from the Task Builder.
• OMX Image Registration: The "most-recently used" parameter files ar now being properly remembered by the software.
• OMX Generate Widefield: This tool no longer fails when specifying a Z subset.
• Arbitrary Profile: The Full-Width Half Max calculation has been improved.
• Stitch: The interactive Stitch tool now has status reporting and Cancel functionality.
• Stitch: Enabling Remove Bright Pixels no longer causes the tool to crash.
• Convolution: Crash when re-using the tool has been fixed.
• Edit Polygon: Closing the input Image Window is now properly handled.

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Version 6.5.2

softWoRx version 6.5.2 is a minor release providing increased reliability and improved functionality. 

Changes and Additions

• OMX SI Reconstruction - Task Builder: Last-used Base OTF files are now tracked by acquisition type (3Beam, 2Beam, 2Beam TIRF).

Software Defects Fixed

• OMX SI Reconstruction - Task Builder: All OTF files are now properly validated against the acquisition type (3Beam, 2Beam, 2Beam TIRF) of the image to be reconstructed.
• Quick Projection, Copy Region, Blend Colors, Image Fusion, Filter 2D, Equalize Time Points: These tools now properly construct output file name suggestions when writing output to an image window.
• DeltaVision Instrument Controller: The Instrument controller now automatically attempts to re-establish communication with the keypad if it becomes disconnected.
• DeltaVision Instrument Controller: Resolve3D should no longer stop writing new data to file in a single z, single channel, fast acquisition (using shutter for each entire scan), and time-lapse experiment.  

Version 6.5.1

softWoRx version 6.5.1 is a minor release providing increased reliability.

Software Defects Fixed

• OMX PSF to OTF: 3Beam PSF files created with pre-6.5.0 software are now properly identified and supported.
• OMX SI Reconstruction - Task Builder: The per-channel Wiener Filter constants are now properly used in 3D / 3Beam reconstructions.
• OMX SI Reconstruction - Task Builder: k0 values should be properly constrained to the range of -PI to +PI radians.
• OMX SI Reconstruction - Task Builder: The Channel Specific OTF Groups tool should now be properly initialized when first opened.
• OMX Image Registration and PSF to OTF tools: Input files containing spaces in the folder or file name are now supported.
• OMX SI Reconstruction tool: An error message appears if the input Image Window has been closed before choosing the Do It button.
• Localization: The Persistence Histogram is now properly updated when changing the input Localization data file.

Version 6.5.0

softWoRx version 6.5.0 provides enhanced functionality and increased reliability.

Changes and Additions

• OMX SI Reconstruction: Support has been added for the processing of 2-Beam 3D, 2D, and 2D TIRF data from OMX. The SI Reconstruction tool will automatically determine the imaging mode that was used to acquire the original data.
• OMX SI Reconstruction: The Drawer dependency for Channel-Specific options has been replaced with Emission channel wavelength dependency.
• OMX SI Reconstruction: Channel-Specific OTF assignments are now organized as user-named OTF Groups.
• OMX SI Reconstruction: The log file produced by the 3 Beam Reconstruction tool now provides a summary of refined k0 and line-spacing parameters found in the k0 search.
• OMX PSF to OTF: The tool now detects whether it's working with 3 Beam or 2 Beam PSF data and then generates a corresponding OTF file.
• OMX Image Registration Calibration: This tool now puts resultant calibration parameters files in a more visible place (HOME_DIRECTORY/softWoRxConfig/) with descriptive names.
• OMX SI Reconstruction and Image Registration: Copies of OTF and calibration parameter files are now saved in a subdirectory (ParameterFiles/) of the folder where the output data is stored. 
• Task Builder: The OMX components of the Task Builder have been updated to the new processing style of the SI Reconstruction and Image Registration tools.
• softWoRx: A Close All menu option has been added to the Window menu of the main softWoRx application to clean up the Desktop by closing all (unsaved) image windows and tools that are attached to them.
• softWoRx: Tooltips have been added to the main menu system to describe what each menu item does.
• Localization: A Persistence (track length) Histogram has been added to aid in evaluating fluorophore tracking results.
• Localization: The Localization Results viewer now allows you to filter the view by maximum localization precision.

Software Defects Fixed

• Localization: Reconstructions referenced to previously-reconstructed images are now rendered with proper coordinate systems.
• Localization: Many problems related to file name handling and drag and drop performance have been fixed.

Version 6.1.3

softWoRx version 6.1.3  is a minor release providing enhanced functionality and increased reliability.

Changes and Additions

• Added 2D, 3Beam SI Reconstruction capabilities to OMX processing
• Now includes a MigrateOMXSettings tool to save and restore OMX-specific user preference settings

Software Defects Fixed

• Generate Widefield from SI Image: This now works properly when selecting a subset of channels, time points, and X,Y region. It is required to specify the entire input Z section range, however.
• SI Reconstruction: The Reconstruction tool no longer fails if a number greater than 99 was entered in a k0 angle field.
• SI Reconstruction: Channel-specific Wiener filter values are now being handled properly when choosing a subset of channels to process.

Version 6.1.2

softWoRx version 6.1.2  is a minor release providing enhanced functionality and increased reliability.

• Updated the driver for the PCO sCMOS camera.

Version 6.1.1

softWoRx version 6.1.1  is a minor release providing enhanced functionality and increased reliability.

softWoRx

• Localization: Localization Analysis is now roughly 2-3 times faster.
• Localization: Localized fluorophores can now be tracked over time and reconstructions can be based on the total intensity of these grouped events.
• Localization: Fiducial markers can now be detected and used to correct images for stage X/Y drift. This method is in addition to the existing Image Correlation drift correction.
• Arbitrary Profile: A simple peak Full-Width Half-Max calculation has been added.
• Resolve3D: More icons have been added to the main control panel to provide more direct access to several capabilities.

Version 6.1.0

softWoRx version 6.1.0  is a minor release providing enhanced functionality and increased reliability.

softWoRx

• Localization: A suite of tools has been added to analyze Localization microscopy images acquired on DeltaVision and OMX systems. Included are methods to localize single-molecule fluorophores, correct for sample drift, and reconstruct super-resolution images from the localization data. These tools will be available if Localization is licensed on the workstation.

DeltaVision Acquisition

• Localization: Single-molecule switching experiments involving multiple activation laser events are now supported. Tools have been created to help design and interact with these experiments as they are running. This experiment mode will be available if Localization is licensed on the acquisition workstation.

Version 6.0.0

softWoRx version 6.0.0  is a major release providing enhanced functionality, improved performance, and improved reliability. This edition of softWoRx 6.0.0 is designed to be used with DeltaVision microscope systems and OMX^TM processing workstations.

Changes and Additions

softWoRx

• Task Builder – File Copy: Changed so that a simple file copy can be the only task. This can be used to enable DropBox capability in the open-source Omero data management system.
• Task Builder – Chromatic Correction: A Chromatic Correction task has been added.
• Point Values and Measure Distance: These tools now optionally display values with sub-pixel resolution to provide better support of Localization Imaging.
• Image Viewer: Functionality has been added to the Montage Display to allow for Color or Grayscale Channel viewing style.
• Save As TIFF: Support for 32-bit floating point format has been added as an option.
• Trails Movie: An option has been added to do a simple Maximum Intensity calculation over time when creating a trails movie.

DeltaVision Acquisition

• Scientific CMOS: Added support for the scientific CMOS camera implemented for its sensitivity, CCD size, and frame rates up to 400 fps for specific experiment types.
• Microscope Control: Added support for the latest-generation Instrument Controller, including its dramatically increased data transfer speeds.
• Experiment Designer: New workflow layout for Design/Run Experiment tool.
• Shutter Selection: All illumination source switching is now handled automatically.
• Panel Collection Focus: Autofocus and focus maintenance (UltimateFocus) can be applied during panel collection.
• Post-Acquisition Processing: Tasks may now be as minimal as copying the image and log files to a different location (enables use of OMERO "DropBox" capability, for instance).
• Find Exposure: The Find Exposure tool is now better optimized for bright InsightSSI^TM illumination.

OMX Support Changes

• Warp Image Alignment: A new algorithm has been implemented to provide more accurate, non-uniform X/Y channel-to-channel image alignment. Z-shifts (expressed in microns) are entered manually and are not restricted to whole-pixel increments.
• Enhancements for Time Lapse Data: These include proper timestamp handling in the SI Reconstruction and options for enabling/disabling k0 angle recalculation for each time point.
• Create Widefield Image: A new tool has been added to create a widefield image from 3D SI data.
• Migrate OMX Settings: A tool has been added for migrating OMX-related softWoRx settings between workstations.

Version 5.5.0

softWoRx version 5.5.0  is a major release providing enhanced functionality, improved performance, and increased reliability.

Changes and Additions

Usability, Visualization, and Analysis

• File Chooser: The Open Image File Chooser now shows the file name list in a way that can be sorted by Date or File Name, ascending or descending.
• File Chooser: You can now select a text file (an R3D log file for instance) with the Open Image File Chooser and it will open the file in a text editor.
• Task Builder: You can now specify a directory (network storage device, for instance) to which input images are to be moved before processing them.
• Task Builder: The OTF file to be used for Deconvolution can now be specified in the Deconvolution Task Options.
• OMX Support: OMX SI Reconstruction, Image Alignment, and OMX OTF tools are now available for appropriately-licensed systems.

Software Defects Fixed

• Montage Display: The Image Window now properly reports coordinates when in Montage Display mode.
• Camera Gain: Due to many complications and unexpected consequences, camera gain can no longer be set to different values for different channels.