WormLab ® 2017 Release Notes
WormLab 2017 was released on June 9, 2017
New features and enhancements
Group Analysis - view data from multiple project files and aggregate data in user defined sets
Swimming Metrics - 10 novel swim behavior metrics reporting dynamic changes in posture and speed*
Enhanced Automated Stimulus Control (Optional Extension Module)
• Time based or frame based stimuli may be defined
• Stimuli intensity control is supported using WormLab hardware
• Plug and Play compatibility: WormLab hardware supports dynamic parameterization of the stimulus interface
• Support for TTL control of external devices
• Preview stimuli display graphically represents your defined stimuli patterns prior to acquisition
Enhanced Label Analysis – labels may be used to display aggregate results (calculated over the entire video) OR split results (results specific to each period of time corresponding to the recurring label)
Support for Mobile Licensing – enables WormLab license to move easily between various computers using a USB license key. Contact MBF Bioscience for details.
Video slider control allows you to quickly scroll through acquired video sequence
Angular direction plots may be viewed in standard mode or you may restrict the angle range +/- 180°
Buffered encoding support – allows the user to specify frame buffer size to encoder short videos at high framerate
New Features and Improvements:
- Save and re-use your tracking settings with the configuration manager.
- Only track the worms currently displayed by adjusting the detection frequency.
- Enhanced curvature map analysis.
- Zooming centered at mouse position.
- The tracking algorithm is now fully multi-threaded and runs significantly faster.
WormLab 4.0 was released on Jan 28, 2016.
New Features and Improvements:
- WormLab can perform tracking of multiple videos without manual intervention. Significantly improves throughput and efficiency.
WormLab labels are used to mark portions of a video in both time and space defined by a 2D graphical overlay (user defined circle or rectangle), a start frame and an end frame.
- Quickly navigate between labelled portions of video using the “Go to label” feature
- Region of interest (xy and t) analysis and tracking. May be used to eliminate artifacts within the field of view or decrease tracking time focusing only within the region or time of interest
- Chemotaxis analysis – a label is assigned to a user defined region and WormLab will provide distance and speed measurement of the worms relative to the labeled area.
Acquisition and Control
- Added support for Basler USB3 Vision cameras
- Precise software control of the WormLab illuminator output
- Support for a new Stimulus Track – manual or automated I/O to correlate external events during video acquisition
Whole Plate Tracking
- Improved whole plate tracking of low resolution worms.
User interface enhancements
- Improved the general User Interface with new icons for workflows and video controls, added context sensitive help buttons and Tooltips.
WormLab 3.5 was released on Oct 7, 2014.
- Long video sequence of more than 10,000 frames are now fully supported. We also dramatically improved our software responsiveness for the display and plotting of very large data tables.
- Our effort to better handle larger data sets associated with longer video sequences is complemented by a new modified project file utilizing a more efficient binary file format. WormLab is capable or reading the original XML project file formats and converting them automatically upon saving to the more efficient binary format.
- If the software cannot locate the video file at the path specified in the project file, it will look for the file in the current directory. If a video file with the appropriate name is located within the directory where the project file is located, the user is then asked if he wants to use this file instead.
- Added unit of measure (Radians or Degrees) to the Direction, Bending Angle (Mid-point and Multiple) plots and histograms and Curvature map.
WormLab 3.1 was released on April 9, 2014.
- The analysis now provides for a Kalman smoothing option to reduce the positional error associated with worm model fit and video jitter. This filter significantly reduces the sporadic, single-frame backward speed for slowly moving worms, giving a more accurate measure of the total track length traveled in both forward and backward directions.
Track Summary Analysis
- Now includes new metrics for: Peristaltic Track Length, Peristaltic Speed and Straight-Line distance.
- This is a new analysis used to report on total time spent going in the forward direction, the reverse direction or remaining idle. The user can set thresholds for the min speed to be considered making forward or reverse progress, and the number of frames such a speed must be maintained. A graphical plot is produced showing the forward and backward mobility overlaid on a plot of the worm speed.
- Head/Tail assignment through coiling, self-overlap and Omega bends
- Enhanced whole plate tracking
WormLab 3.0 was released on Oct 10, 2013. This major release contains a significant number of new features.
- We have added a full set of interactive plotting and reporting tools to create line charts and histograms based on worm position and shape data. This includes 18 analyses and 6 histogram summaries. The new analysis window contains a list of selectable analyses, a data table display area and a charting area. The data can be exported to excel, and the charts can be copied to your clipboard or saved in common image file formats or in PDF format. The charts are customizable for color and text and support zoom and pan operations to examine the data.
- Track multiple swimming worms at once. We've added a new fitting model specifically for swimming worms. You'll find a the option in the Tracking step offering a choice between crawling and swimming mode.
Hot Spot Correction
- For larger fields of view under a microscope or camera stand, the light source often creates a brighter spot at the center of the light source. WormLab now contains a specific filter to flatten the light field. The background light is modeled by the software and removed from the image. The result is better tracking across the hotspot light gradient. This is completely automatic when turned on and applies to vides already captured.
- The Video view and the Analysis view are now synchronized. Click on a row in the analysis data table, and the video jumps to the same frame. Move the video frame slider and the data view moves to the appropriate frame in the table. This makes it much easier to quickly match the worm shape metrics with the video visualization.
Video Capture Duration
- If you have the optional Video Capture Module with WormLab, then you'll notice that you can now set the time duration for acquisition. This helps when capturing short sequences of video where you require each sequence to be the same length of time (e.g. 1 minute).
Video Capture : Clipping
- When setting the camera exposure, it's best to attempt to maximize the dynamic range. You can do this by limiting the amount of overexposure. The Clipping check box will show you the parts of the image that are overexposed. Shorten the exposure time or closing down the lens aperture can reduce the overexposure.
- We've made general improvements in the User Interface (UI), including new icons, reduction of the workflow by one step, and redesign of the Video Capture window. We've also made the Analysis window its own standalone window owing to its larger size.
Repair: Join Tracks
- It's now possible to join multiple tracks together at one time. Enter a list of tracks to join together, separated by commas.
Editing & Redection
- You can now delete part of sequence of worms and redetect those worms with either single-click detection or manual tracing detection. The software automatically joins the worm to the appropriate track.
- The display has been modified to show the threshold settings as green worms on the image background. This replaces the black-and-white view previously used, making it easier to set a correct threshold.
Tools Menu: Snapshot
- You can now also export portions of a video as a sequence of still images or a video file.
- All data tables in the Analysis window display both frame number and now time-point where appropriate.
WormLab 2.3.0 was released on June 14, 2013.
Feature Modified: We modified the Swap head/tail feature on the “Repair” tab. There are now two ways to swap:
- Swap head/tail for the entire track (same as version 2.2)
- Swap head/tail from the current frame to the end of track (new)
- We added this second option to repair tracks where the head/tail is incorrectly swapped after a worm emerges from an omega bend. This is easier and faster than the previous way of splitting the track, swapping head/tail on the secondary track and then rejoining.
WormLab 2.2 was released on April 30, 2013.
Tracking - Speed Optimization: Changes were made to optimize the initialization of tracking for each video frame. This change improves speed, decreases memory usage but does not change the tracking results.
Camera - AVT Format-7: WormLab now supports larger image formats using Format-7. This allows for full frame use of the AVT-Stingray-F504B/C cameras, as well as other DCAM/IIDC compliant cameras with large image sizes. This only affects WormLab systems with the optional Camera Interface module.
Camera - Firewire A/B Fallback: The camera interface will fall back to the slower Firewire A (400 Mbps) if the connection to Firewire B fails.
Camera - Connect/Disconnect: WormLab now supports camera connection/disconnection while the application is still running.
Camera - Video File Write: We improved the speed of video writing, which now supports faster frame rates and larger image frame sizes. The throughput still depends on the processing and I/O speed of your computer.
Camera - Exposure Display: For cameras that support this feature, WormLab now displays the correct exposure setting time units.
WormLab 2.1 was released on Jan. 25, 2013.
Centerline points analysis: WormLab can now export multiple points in (x,y) coordinates along the worm centerline. The user can choose the resolution as a number of points to sample along the spline basis centerline. The data is available as an export to Microsoft Excel, in .CSV (comma separated value) format and can be imported into third party products such as Matlab® by The Mathworks.
Multi-point bending analysis: This analysis provides a measurement of the bending angle at multiple points along the worm centerline. The centerline is modeled as a spline basis, and the user can choose the number of points to sample from this curve. The bending angles are exported in either radians or degrees, and an angle of 0.0 indicates no bend.
Video snapshot: With the optional Camera Capture Module, WormLab can save a snapshot of the view through the camera while simultaneously recording video. This feature is useful for capturing a still-image of the scale bar or for making a record of interesting events that appear in the view finder while recording.
WormLab 2.0 New Features
WormLab 2.0 was released on Nov. 1, 2012.
Apple Mac OSX® Version
- WormLab is now available on the Mac®. This new version software is designed for the native Mac user interface and runs just as quickly and accurately as the Microsoft Windows ® version with identical tracking results.
Extensive Camera Support
- WormLab has an optional Video Capture module designed to making the capture and processing of worm videos simple and efficient. The capture module offers streamed-capture or time-lapse-capture with intervals as short as 1/4 second. In WormLab 2.0, we've updated the interface to support the IIDC standard (Instrumentation and Industrial Digital Camera) for Firewire IEEE 1394. There are now over 1400 different camera models supported by WormLab, including cameras from Point Grey and Allied Vision Technologies (AVT). Contact MBF to see if you interested in purchasing a camera with WormLab or to check if WormLab supports your existing camera.
Faster Tracking and Improved Accuracy
- We’ve improved our tracking algorithms for version 2.0, particularly through self-overlap and entanglement. We've also added options to turn on/off width and length fitting—options that help improve tracking performance and accuracy through entanglement. Tracking is much faster throughout, and the 64-bit version is even faster than the 32-bit version.
Whole Plate Mode
- WormLab now includes an option to track many worms on a plate captured at low magnification. This new mode runs faster than regular tracking. The difference is that worms are tracked up to the point that they interact (touch, cross) and tracking resumes when entanglement ends.
New Data Export
- This new version now exports data to .CSV files, opening up more options to use and analyze your data with more third-party software such as Microsoft Excel®. We have included examples demonstrating how to import your data into MATLAB® (MathWorks®, MA), a popular software program for data analysis used by many of our customers.
- This new version of the software includes reporting on the shape of the worm centerline, exported as a set of coordinate points. You can choose the number of sample points along the worm centerline and which track to analyze. We've even included an example of how to import this data into MATLAB and create a simple plot animating the worm centerline.
Track Editing (Join/Split)
- New options are now available to join separate worm tracks. This is useful when tracking of a worm drops due to imaging, but picks up a few frames later. Our tracking in 2.0 is smarter and joins split tracks automatically—but if two tracks aren’t connected properly, use this tool to manually join these tracks.
Manual Worm Trace
- For difficult to detect worms, you can use the mouse to trace the worm centerline from head to tail by clicking just a few points, giving WormLab a very strong hint on the shape of the worm for better detection. WormLab 2.0 automatically connects manually traced worms onto the appropriate track from adjacent video frames.
Still Easy to Use
- Many of our customers have remarked how easy it is to download and start using WormLab . The new version features the same intuitive step-by-step workflow, from loading or capturing videos through to data analysis and export. Our excellent customer support can help you with tracking and improving your video capture techniques.
Windows 8 Ready
- If you are running Windows 8, then you'll find that WormLab 2.0 works just fine (we suggest using the 64-bit version).