Workflow | BIII

A workflow is a set of components assembled in some specific order to

Measure and estimate some numerical parameters of the biological system or
Visualization

for addressing a biological question. Workflows can be a combination of components from the same or different software packages using several scripts and manual steps.

Measuring confluence in adherent cell cultures

Workflow

Description

This publication describes a very simple protocol to acquire images of adherent cell cultures over time and how to process these images in ImageJ to measure the area fraction (confluence).

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Interactive Density Counting using ilastik

Workflow

Description

This workflow estimates (densely distributed) object counts by the density of objects in the image without performing segmentation or object detection. Current version only works for 2D images of roundish objects with similar sizes on relatively homogeneous background. Users should provide a few labels of background and objects (especially on clustered objects), and the tool predicts the density of objects on the entire image. Counting is then estimated by integrating the density values on the whole image or specified rectangular regions of interests.

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Artemia color analysis

Workflow

Description

The Artemia Tools help to calculate the normalized redness of Artemia in color images.

See: http://dev.mri.cnrs.fr/projects/imagej-macros/wiki/Artemia_Tools

Test images: http://biii.eu/node/1139

has topic

Bioimage informatics

has function

Object feature extraction

Human cytoplasm-nucleus translocation assay using CellProfiler

Workflow

Description

In this human cytoplasm-nucleus translocation assay, learn how to load a previously calculated illumination correction function for two separate channels, measure protein content in the nucleus and cytoplasm, and calculate the ratio as a measure of translocation. This is a clumpy cell type, so studying the settings in primary object identification may be helpful for users interested in the more advanced options that module offers. More about these images can be found at the BBBC.

has topic

Bioimage informatics

Fluorescence microscopy