MaMuT

Description

MaMuT is an end user plugin that combines the BigDataViewer and TrackMate to provide an application that allow browsing, annotating and curating annotations for large image data.

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Description

The purpose of the workflow is ....

First you need

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QuimP

Description

Summary

QuimP is software for tracking cellular shape changes and dynamic distributions of fluorescent reporters at the cell membrane. QuimP's unique selling point is the possibility to aggregate data from many cells in form of spatio-temporal maps of dynamic events, independently of cell size and shape. QuimP has been successfully applied to address a wide range of problems related to cell movement in many different cell types. 

Introduction

In transmembrane signalling the cell membrane plays a fundamental role in localising intracellular signalling components to specific sites of action, for example to reorganise the actomyosin cortex during cell polarisation and locomotion. The localisation of different components can be directly or indirectly visualised using fluorescence microscopy, for high-throughput screening commonly in 2D. A quantitative understanding demands segmentation and tracking of whole cells and fluorescence signals associated with the moving cell boundary, for example those associated with actin polymerisation at the cell front of locomoting cells. As regards segmentation, a wide range of methods can be used (threshold based, region growing, active contours or level sets) to obtain closed cell contours, which then are used to sample fluorescence adjacent to the cell edge in a straightforward manner. The most critical step however is cell edge tracking, which links points on contours at time t to corresponding points at t+1. Optical flow methods have been employed, but usually fail to meet the requirement that total fluorescence must not change. QuimP uses a method (ECMM, electrostatic contour migration method (Tyson et al., 2010) which has been shown to outperform traditional level set methods. ECMM minimises the sum of path lengths connecting all pairs of points, equivalent to minimising the energy required for cell deformation. The original segmentation based on an active contour method and outline tracking algorithms have been described in (Dormann et al., 2002; Tyson et al., 2010; Tyson et al., 2014).

Screenshot

Cell segmentation in phase contrast images

Description

This Matlab code demonstrates an edge-based active contour model as an application of the Distance Regularized Level Set Evolution (DRLSE) formulation.

initialisation

Measure cell volume over time

Description

The workflow measures the growth of cells in 3D, combining an ImageJ macro for preprocessing and successive tracking using Imaris.  

The sample dataset (available in the github repository) contains 2-Photon images of neurons. The neurons were imaged in 3D at two time frames.To allow measuring significant differences in cell volume, the time gap between the frames is large (ca. 30 min) and the animal was removed in the waiting phase. For this reason, there is a considerable shift in sample position between the frames that has to be corrected before cell detection and tracking.

The workflow consists of following steps:

1. Import of single tiff slices [imageJ macro]

2. Organizing the data in a 4D time series with 2 time frames [imageJ macro]

3. Correction of shift between the time frames by rigid registration [imagJ macro]

4. Bleaching correction [imageJ macro]

5. Export of preprocessed image data in ics/ids format [imageJ macro]

6. Import of ics/ids data to Imaris [Imaris]

7. Cell object detection as "Imaris Surface Object" [Imaris]

8. Tracking cell objects over time [Imaris]

9. Split Tracks (use Imaris XT extension "Split Tracks") to generate single cell objects [Imaris]

10. Export the statistics: Select the complete folder, go to the statistics tab and use ‚Full Export’ [Imaris]

The preprocessing macro can be referenced here: [![DOI](https://zenodo.org/badge/7683/cmohl2013/registration_and_bleaching_corr…)](http://dx.doi.org/10.5281/zenodo.13167)

The sample images were acquired by Cordula Ulbrich (Petzold Group at German Center of Neurodegenerative Disesases (DZNE), Bonn, Germany).

Input data type: tiff

Output data type: data table

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2D cell tracking and analysis of morphological dynamics

Description

The QuimP software from Bretschneider group is deployed as ImageJ plugin and includes model-based cell segmentation, cell outline tracking and quantification of the spatially resolved speed of protrusions and retractions. The algorithm to calculate morphological dynamics is faster compared to other approaches (e.g. Machacek and Danuser, 2006). The reference paper describes the workflow for these analyses.

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Track cell intensity

Description

Tracks a cell in a 2D video using active contours, and produces a list of ROI where intensity is measured and reported into a workbook. The cell must be first delineated with a ROI in the first image of the video.

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Oufti

Description

Oufti (previously named MicrobeTracker) is a MATLAB application / suite of tools for analysing fluorescent spots inside microbes. MicrobeTracker can identify cell outlines and fluorescent foci, and generate plots and statistics based on positions and intensity (kymographs, histograms etc.) The MATLAB code is easy to modify and extend to add additional plots and statistics: see e.g. Lesterlin et al. (2014).

The Outfi Forum is quite active.

Object Tracking and Metadata Management

Description

The goal of this workflow is to track cells captured in a time-lapse movie of a syncytial blastoderm stage Drosophila embryo and quantify their movement.

This example shows an example of object tracking. This pipeline analyzes a time-lapse experiment to identify the cells and track them from frame to frame, which is challenging since the cells are also moving. In addition, this pipeline also extracts metadata from the filename and uses groups the images by metadata in order to independently process several sequences of images and output the measurements of each.

Sample images

A portion of a time lapse movie of a syncytial blastoderm stage Drosophila embryo with a GFP-histone gene which renders chromatin fluorescent in live embryos. The movie shows nuclear divisions 10 through 13.

Victoria Foe made this movie on a Bio-Rad Radiance 2000 laser scanning confocal microscope using a 40X 1.3NA oil objective. The frames are 7 seconds apart and plays at 30 frames per second

GFP-histone transformed files provided by Rob Saint

V.Foe and G.Odell, . 26 July 2001

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