Good news, Bio Image Operation is now available as Open Source on GitHub

https://github.com/folterj/BioImageOperation

Click here for the feature video

The latest release of Bio Image Operation (BIO) is available here.

BIO is only released as 64 bit, requiring a 64 bit version of Windows.

Download BIO version 1.4.420.22

Download BIO script instructions

Version 1.4.420.22:

- Support OpenCV 4.2.0 (and correct version of openh264)

- Save clusters/tracks: now uses frames and time as well as saving contours, added different output formats

- Fixed various small bugs

Version 1.4.410.21:

- Fixed memory leak in showing images with stride

- Use time when saving tracks etc

- Proper file modified detection including auto save on run

Version 1.4.410.20:

- Support OpenCV 4.1.0

- Fixed bug in videos without length/frames property

- Fixed bug showing images with stride/padding

- Fixed bug not showing images after error occurs

- Minor fixes for video progress

Version 1.4.400.10:

- Added saving clusters and tracks by label

Version 1.4.400.9: 

- Exposed video API selection

Version 1.4.400.8:

- Supports OpenCV 4.0.0

- Fixed bugs in image series and cluster drawing

- Simplified stats calculations improcing automatic tracking parameter calculation

Version 1.4.341.7:

- Added GPL license information

Version 1.4.341.6:

- Further improved automatically finding optimal tracking parameters

- Added 'Check for updates' functionality

- Minor bug fixes

Version 1.4.341.5:

- Significantly improved automatically finding optimal tracking parameters

- Draw logarithmic color legend based on input parameters

- Many improvements and bug fixes and updates to the help/manual

Version 1.4.341.4:

- Implemented directly writing to video file using H264 encoding

Version 1.4.341.3:

- Significant improvement in overall performance

Version 1.4.341.2 (OpenCV 3.4.1):

- Implemented all track draw functions including many options

- Improved script argument checking and help

- Uses OpenCV 3.4.1

Version 1.4.34.1 (OpenCV 3.4) - This is a major rewrite from C#/Emgu to C++/OpenCV. These are the key points:

- Using OpenCV directly - with full library support and using the latest version

- Real-time processing of HD video source (on standard consumer hardware) due to significant performance improvements

- Direct memory management with superior memory footprint

- Improved error handling and argument checking

- Built-in dynamically-generated script help

- Improved cluster detection: using connected components for accurate cluster sizes

- Very efficient custom image display, for minimal impact on main image processing loop

- Improved installer with pre-requisites detection and download (using WiX)

- Re-branded artwork

Flexible Script-based Image Operation

Bio Image Operation or 'BIO', is a next generation Image processing tool focussing on biological applications, balancing ease of use with desired flexibility required for research.

This tool has been developed in collaboration with biologists, using extensive captured images.

The solution balancing both the need for research purposes and flexibility required for this, and desired ease of use is realised in a script based user interface.

The tool uses the widely used OpenCV for many of it's image operations, with an efficient tracking algorithm allowing real time processing (upto HD @ 50 fps).

Automated tracking example: Tracking from public source: ants walking on concrete with varying lighting (video used from this public source):

(View full video here)

User Interface

Visualisation example

Visualising tracks simply using image combination (Source material from Tom Wenseleers and colleagues - University of Leuven)