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Labview

Collection
Description
A commercial software traditionally used in Industry and Engineering/Science to enable fast software development and deployment of a very broad range of devices control. Labview enables graphically oriented programming (no text-based coding) and offers many ready-made tools to perform basic tasks on complex data (including image data), maths operation, data handling and representation. For Image processing and analysis, Labview offers the integrated "NI Vision" tool, used in image-based quality control of production lines with a broad selection of Image-based filters/operations. In microscopy, Labview can be used efficiently to perform any kind of instrument control, and in particular "Feedback Microscopy" (also called intelligent microscopy, etc...) where the live analysis of a captured image will update the target of the microscope to make it understand where to image efficiently.
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Skeletonize

Component
Description

ImageJ native "Skeletonize" implementation. - works only with 8-bit binary image. A faster implementation is available as a plugin Skeletonize3D written by Ignacio Arganda-Carreras. Pros of this plugin is summarized here.

has topic
Bioimage informatics
has function
Object feature extraction
Morphological operation
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Angiogenesis Analyzer for ImageJ

Workflow
Description

Quote:

The "Angiogenesis Analyzer" allows analysis of cellular networks. Typically, it can detect and analyze the pseudo vascular organization of endothelial cells cultured in gel medium

...a simple tool to quantify the ETFA (Endothelial Tube Formation Assay) experiment images by extracting characteristic information of the network.

The outputs are network feature parameters.

Sample images

http://image.bio.methods.free.fr/ij/ijmacro/Angiogenesis/HUVEC-Pseudo-Phase-Contrast.tif.zip

http://image.bio.methods.free.fr/ij/ijmacro/Angiogenesis/HUVEC-Fluo.tif.zip

Source code

https://imagej.nih.gov/ij/macros/toolsets/Angiogenesis%20Analyzer.txt

has topic
Imaging
has function
Image analysis

FibrilTool

Component
Description

Evaluates the orientation of fiber orientation pattern and plots the results in the image. It calculates gradient in x and y direction. - then calculates the eigenvector of nematic tensor, which is the orientation of the pattern.

has topic
Microscopy
Statistics
has function
Frequency analysis
Filament tracing
Interactive segmentation

ImageJ Plugin LineageTracker

Component
Description

## Short Summary Quote from the plugin page: >LineageTracker offers an ImageJ based framework which is easily extendible and has the capability to track cell lineages while being specifically designed to handle large cell displacements between frames. The methods are designed for fluorescent cells and have been used to analyse Schizosaccharomyces pombe, C2C12 mouse stem cells or migrating RPE cells. This tool also allows flexible cell segmentation and extendable in all aspects. The webpage is detailed with usage from ImageJ macro. Rather than being simply a component, the plugin is indeed a framework with set of components. ## Misc info A tip from the plugin author in ImageJ mailing list (08.Sep.2015): > We have an additional script to export only a selected range of frames. I can send you that if you think LineageTracker is something for you. To be on the safe side I would try it with an older version of ImageJ. We have experienced some problems, mostly related to Java. Java 8 seems to fix most of it. ## References 2630: Application example. 2631: Plugin Paper.

has topic
Bioimage informatics
Fluorescence microscopy
has function
Cell tracking
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