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2D cell tracking and analysis of morphological dynamics

Workflow
Description
has function
Cell segmentation
Active contours
Cell tracking

Image anonymisation

Workflow
Description
This macro copies all images from one folder to another, randomizing names but keeping channels from the same image grouped. This is useful for blind quantification of images.
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Optical Flow

Component
Description

This protocol computes the optical flow of a 2D+T sequence. The results are displayed with flow arrows painted on top of the original sequence, and also with two additional sequences for the norm of the flow and a color-coded presentation of the flow following the Middlebury convention.

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LIF Projector

Component
Description

This macro is similar to the LIF_Extractor, but it will output Z-projection of each Z-stack. You can choose the type of projection in addition to the other options. Requires Bio-Formats plugin

has function
Image projection

3D estimation of synaptic vesicle distribution in serial section TEM (ssTEM)

Workflow
Description
An estimate of the shortest distance of vesicles to synaptic cleft is computed in 3D for serial section TEM. Unfortunately the the authors do not provide an implementation. Method: 1. Bias correction for inhomogene lighting 2. Image registration of TEM sections / stacks 3. Detection of vesicles & synaptic cleft (semi-automatic) 4. Compute distances in 3D
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