Image segmentation

Image segmentation is (one of) the (few) concept(s) on the border between Image (pre)processing (Image->Image) and Image analysis (Image->Data).

Description

Machine Learning made easy

APEER ML provides an easy way to train your own machine learning
models and segment your microscopy images. No expertise or coding required.

APEER

Image Analysis Training Resources

Submitted by Perrine on Wed, 06/30/2021 - 14:15

This is a resource for image analysis training material, with a focus on research in the life sciences.

Currently, this resource is mainly meant to serve image analysis trainers, helping them to design courses. However, we might add more text (or videos) to the material such that it could also be used by students for self-directed study.

Description

This tool allows to analyze morphological characteristics of complex roots. While for young roots the root system architecture can be analyzed automatically, this is often not possible for more developed roots. The tool is inspired by the Sholl analysis used in neuronal studies. The tool creates a binary mask and the Euclidean Distance Transform from the input image. It then allows to draw concentric circles around a base point and to extract measures on or within the circles. Instead of circles, which present the distance from the base point, horizontal lines can be used, which present the distance in the soil from the base-line. The following features are currently implemented:

  • The area of the root per distance/depth.
  • The number of border pixel per distance/depth, giving an idea of the surface in contact with the soil.
  • The maximum radius per distance/depth of a root, measured at the crossing points with the circles or lines.
  • The number of crossings of roots with the circles or lines.
  • The maximum distance to the left and the right from the vertical axis at crossing points with the circles or lines.
Concentric circles on the mask of a root, created by the Analyze Complex Roots Tool
Description

webKnossos is an open-source data sharing and annotation platform for tera-scale 2D and 3D image datasets.

The core features of webKnossos are:

  • fast 3D data streaming
  • share links to specific locations in the data
  • uniquely fast skeleton annotation (flight mode) and
  • efficient volume annotation
  • mesh rendering
  • collaboration and sharing tools

webKnossos facilitates image analysis workflows on multi-terabyte datasets, including visualization of raw and multi-modal microscopy data, distributed training data generation and proof-reading of automatic segmentation.

As a scientific resource, webknossos.org serves as a database for published image datasets including their annotations.

 

 

Description

ImageM integrates into a GUI several algorithms for interactive image processing and analysis. Interface is largely inspired from the open source software "ImageJ".

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