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Interactive Density Counting using ilastik

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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VSI File Extractor (ImageJ)

Component

Description

This tool allows for extraction of image series from Olympus Slide Scanners. These VSI files usually contain several images that are too big to load into memory (>50k x 50k pixels). It was written and tested on Fiji and is available from a Fiji Update Site: http://fiji.sc/List_of_update_sites

has topic

Bioimage informatics

has function

Data handling

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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