Release v2.2

Important update, please run setup_conda_env.bat to reinstall the environment.

Major updates

Dependency

• Python 3.8+ will be used for this and later version of ACT to accommodate the required packages.
• pyqtgraph is no longer included locally.
• Several packages had been upgraded or downgraded to avoid dependency clash.

Algorithm

• Skan package will be used as the primary length calculation package for clusters detected from super-resolution images. Both main branch length and total branch lenght will be reported. However, measuring length of the skelentonized cluster is not ideal for dot-like/round particles, it would be more accurate to use the major axis length in this case.

Fixed bugs and improvements

Diffraction limited image analysis

• Fixed error raised when loading result of a previous analysis.

Super resolution image analysis

• Removed redundant lines in cluster analysis. Fixed error when only 1 cluster present.
• Fixed image not closed after SR drift correction.
• Provided alternative method to check SR image frames

Liposome Assay analysis

• Fixed error caused by dependency updates.
• Included progress bar in prompt for samples.
• Changed result folder naming.

Miscellaneous

• Setup batch now will remove the existed ACT_python3 environment before build.
• Fixed UI connections.
• Muted FutureWarning from pandas.
• Updated simulation codes.

Release v2.1 - ACT Publication

Stable release of ACT for publication on Cell Reports Methods.
ACT: A Computational Suite for the Structural and Functional Characterisation of Amyloid Aggregates

Major bug fixed - SR - Cluster profiling

An error was reported for the cluster profile result calculated from the super-resolution analysis. The empty row and column in the reconstructed images with cluster id were droped. This led to a wrongly calculated cluster size, area, eccentricity, and hence length calculation. The error is fixed in this release.

Full Changelog: v2.0.1...v2.0.2

Release v2.0.1

1. Improved error handling in SR analysis:
   a. Skip the images which were damaged - failed to be loaded by imagej.io.
   b. Fixed output type when result with no localisation was encountered. Avoided mission abort when no localisation or cluster detected in a field of view.
2. Fixed no response of UI when trying to cluster a dataset which was not super-resolved.

Release v2.0

Version 2 development completed

Features

1. Particle detection from diffraction limited images
   • ComDet method
   • PyStar method
2. Super-resolution image analysis
   • Image reconstruction with GDSC SMLM 1 and ThunderStorm
   • Drift correction with Cross-correlation and Fiducial correction
   • DBSCAN for cluster analysis
   • Particle profiling and length calculation
3. Liposome assay analysis
4. Tools
   • Splitting images into multiple folders based on file names

Updates

1. Updated python environment installation method
2. User interface clean up
3. Changed the program name to Aggregate Characterization Toolkit

Release v1.2.1

New feature:
Super-resolution image analysis

Debug:

1. Diffraction-limit analysis edge particle removal parameter
2. Diffraction-limit analysis method Trevor parameter

Release v1.1.1

1. Enabled multiprocessing for Liposome assay.
2. Minor bug correction.

Beta release for super-resolution image analysis

This is a pre-release containing function that may not work fully as expected.
This pre-release does not contain features updated in v1.1.0 onwards.

1. ThunderSTORM:

   • Image reconstruction
   • Fiducial correction with autocorrelation
   • Fiducial correction with fiducial markers

2. GDSC SMLM 1:

   • Image reconstruction

3. Bug correction:

   • The wrong parameters were assigned for the diffraction-limited image analysis method Trevor.

Release v1.1.0

New features/improvements

Included liposome assay analysis in UKIA.

Upcoming features/improvements

1. Improvement of orthogonal analysis.
2. Single molecular image analysis.

Release v1.0.1

1. ComDet - Remove edge particles detected.
2. Trevor - Enabled multiprocessing.