ACT - Aggregate Charaterization Toolkit

A platform for the rapid analysis of both diffraction-limited and single-molecule localisation images.

Applications

• Diffraction-Limited Analysis

  This program is intended for the rapid analysis of diffraction-limited images generated under fluorescence microscope. It is capable of distinguishing and characterising the protein aggregates (or other targets) captured on surface.

  Two methods are available:

  1. ComDet - This method relies on Fiji(is just imagej) and ComDet - a plugin written by Eugene Katrukha at the Utrecht University.

  2. PyStar - A pure python alternative for the ComDet. (Written by Yunzhao Wu)

  An advanced thresholding method, Orthogonal Analysis, is provided. It can help you to distinguish the actual particles detected from the backgroud noises by setting a threshold based on the 'intensity per area' distribution of the spots.

• Super-resolution Image Analysis

  Super-resolution images are stack of images taken when the fluorescent indicator being constantly bound and dissociated from the targets captured on the surface. This feature provides two image reconstruction methods - GDSC SMLM 1 and ThunderSTORM to track the fluorescent spot through the stack and reconstruct into a image with higher resolution than diffraction limit.

  After image reconstruction, drift correction and particle clustering methods are also provided in the program, allowing you to further characterise the targets detected.

• Liposome Assay Analysis

  This workflow is the improved version of Calcium Influx Assay. It is an automated analysis program for Ultrasensitive Measurement of Ca2+ Influx into Lipid Vesicles Induced by Protein Aggregates developed at the Klenerman Group.

Requirements

Full list please see ACT_python3.yml.

• Python 3 (configured with Python 3.8.16)

  • astropy - 5.2.2
  • imageio - 2.31.1
  • imglyb - 2.1.0
  • maven - 3.6.3
  • numpy - 1.24.3
  • opencv-contrib-python - 4.7.0.72
  • openjdk - 8.0.332
  • pandas - 1.4.1
  • pathos
  • pillow - 9.5.0
  • psutil
  • pyimagej - 1.0.2 (must install with conda-forge)
  • pyqtgraph - 0.13.3
  • PySide 6 - 6.5.1
  • scikit-image - 0.19.3
  • scikit-learn - 1.2.2
  • scipy - 1.10.1
  • scyjava - 1.9.0
  • skan - 0.11.0
  • tifffile - 2023.4.12
  • tqdm - 4.65.0

• Fiji(is just imagej)

  • ComDet
  • GDSC SMLM 1
  • ThunderSTORM

Installation

Please install Anaconda for environment management.

cd /path-to-folder/
setup_conda_env.bat

Usage

The program only supports Windows system for now

Command line tool:

conda activate ACT_python3
python /path_to/main.py

Contributors

Zengjie Xia (University of Cambridge)

Yunzhao Wu (University of Cambridge)

Copyright 2021 Zengjie Xia, at the University of Cambridge.