Image segmentation

This macro was designed to measure the size of the scratch wound in a wound scratch assay. It uses an edge-detection and thresholding technique.

It will batch process all images in a directory. Images captured by time-lapse should be compiled into stacks using a tool similar to "Metamorph nd & ROI files importer (nd stack builder)" by Fabrice P. Cordelières. Images to be analyzed should be placed in one directory (Source Directory). A second directory should be created to save results files and images (Destination Directory). Setting correct Lower and Upper thresholds is important to obtain a good result. Two macros are available, one using edge detection, the second one using background subtraction.

ITK-SNAP is a software application used to segment structures in 3D medical images. It can also be used as a 3D annotation tool for deep learning. It is based on ITK, VTK libraries.

**Collaborative Annotation Toolkit for Massive Amounts of Image Data** CATMAID is a Collaborative Annotation Toolkit for Massive Amounts of Image Data. It is designed to navigate, share and collaboratively annotate massive image data sets of biological specimens. The interface is inspired by GoogleMaps, with which it shares basic navigation concepts, enhanced to allow the exploration of 3D biological image data acquired by optical or physical sectioning microscopy techniques. The interface enables seamless sharing of regions of interest through bookmarks and synchronized navigation through multiple registered data sets. With massive biological image data sets it is unrealistic to create a sustainable centralized repository. A unique feature of CATMAID is its partially decentralized architecture where the presented image data can reside on any Internet accessible server and yet can be easily cross-referenced in the central database. In this way no image data are duplicated and the data producers retain full control over their images. CATMAID is intended to serve as data sharing platform for biologists using high-resolution imaging techniques to probe large specimens. Any high-throughput, high-content imaging project such as gene expression pattern screens would benefit from the interface for data sharing and annotation.

Acquiarium is for carrying out the common pipeline of many spatial cell studies using fluorescence microscopy. It addresses image capture, raw image correction, image segmentation, quantification of segmented objects and their spatial arrangement, volume rendering, and statistical evaluation. It is focused on quantification of spatial properties of many objects and their mutual spatial relations in a collection of many 3D images. It can be used for analysis of a collection of 2D images or time lapse series of 2D or 3D images as well. It has a modular design and is extensible via plug-ins. It is a stand-alone, easy to install application written in C++ language. The GUI is written using cross-platform wxWidgets library.

ITK is an open-source, cross-platform system that provides developers with an extensive suite of software tools for image analysis.

Developed through extreme programming methodologies, ITK employs leading-edge algorithms for registering and segmenting multidimensional data. It is widely used and contributed in the medical imaging field.

Strengths

Highly optimized C++, well commented Consistently updated (new) algorithms many tools and softwares are built upon it connected with VTK Insight Journal (open code and sample data) Extensive list of examples & tutorials

Limitations

yet detached from the bioimage analysis world hard to use for end users without development skills