TEM ExosomeAnalyzer

Description

TEM ExosomeAnalyzer is a program for automatic and semi-automatic detection of extracellular vesicles (EVs), such as exosomes, or similar objects in 2D images from transmission electron microscopy (TEM). The program detects the EVs, finds their boundaries, and reports information about their size and shape.

The software has been developed in terms of project MUNI/M/1050/2013 and supported by Grant Agency of Masaryk University.

The EVs are detected based on the shape and edge contrast criteria. The exact shapes of the EVs are then segmented using a watershed-based approach.

With proper parameter settings, even images with EVs both lighter and darked than the background, or containing artifacts or precipitated stain can be processed. If the fully-automatic processing fails to produce the correct results, the program can be used semi-automatically, letting the user adjust the detection seeds during the intermediate steps, or even draw the whole segmentation manually.

screen capture from exosomeAnalyzer

@msdanalyzer

Description

Mean square displacement (MSD) analysis is a technique commonly used in colloidal studies and biophysics to determine what is the mode of displacement of particles followed over time. In particular, it can help determine whether the particle is:

  • freely diffusing;
  • transported;
  • bound and limited in its movement.

On top of this, it can also derive an estimate of the parameters of the movement, such as the diffusion coefficient.

@msdanalyzer is a MATLAB per-value class that helps performing this kind of analysis. The user provides several trajectories he measured, and the class can derive meaningful quantities for the determination of the movement modality, assuming that all particles follow the same movement model and sample the same environment.

has function
Examples of tracks to perform MSD analysis.

ATLAS Vesicle segmentation method

Description

Part of ATLAS software

Comment / Instructions: 

You can upload your image at the Mobyle@SERPICO portal and download the result. The workflow is only available online, i.e. no download possible.

Interaction Analysis

Description

This plugin can be used for inferring spatial interactions between patterns of spot-like objects in images or between coordinates read from a file. 

Track Manager

Description

The track manager enables the use of DSP-like trackProcessors. This can affect the display of tracks, selection in time or by ROIs, and also compute some views like the overlaid and animated local flow graph, polar graph.

has function

Track Processor Intensity Profile

Description

A TrackProcessor that allows the user to monitor, visualize, and export, the intensity profile of tracks in time lapse sequences of 2D images.

has function
need a thumbnail

TrackMate

Description

TrackMate provides the tools to perform single particle tracking (SPT). SPT is an image analysis challenge where the goal is to segment and follow over time some labeled, spot-like structures. Each spot is segmented in multiple frames and its trajectory is reconstructed by assigning it an identity over these frames, in the shape of a track. These tracks can then be either visualized or yield further analysis results such as velocity, total displacement, diffusion characteristics, division events, etc...