ilastik is free

open source Open source is source code that is made freely available for possible modification and redistribution. Products include permission to use and view the source code, design documents, or content of the product. The open source model is a decentrali ...

software for

image classification Computer vision tasks include methods for acquiring, processing, analyzing, and understanding digital images, and extraction of high-dimensional data from the real world in order to produce numerical or symbolic information, e.g. in the form o ...

and segmentation. No previous experience in image processing is required to run the software. Since 2018 ilastik is further developed and maintained by Anna Kreshuk's group at

European Molecular Biology Laboratory The European Molecular Biology Laboratory (EMBL) is an intergovernmental organization dedicated to molecular biology research and is supported by 29 member states, two prospect member states, and one associate member state. EMBL was created in ...

Features

ilastik allows user to annotate an arbitrary number of classes in images with a

mouse A mouse (: mice) is a small rodent. Characteristically, mice are known to have a pointed snout, small rounded ears, a body-length scaly tail, and a high breeding rate. The best known mouse species is the common house mouse (''Mus musculus'' ...

interface. Using these user annotations and the generic (

nonlinear In mathematics and science, a nonlinear system (or a non-linear system) is a system in which the change of the output is not proportional to the change of the input. Nonlinear problems are of interest to engineers, biologists, physicists, mathe ...

) image

features Feature may refer to: Computing * Feature recognition, could be a hole, pocket, or notch * Feature (computer vision), could be an edge, corner or blob * Feature (machine learning), in statistics: individual measurable properties of the phenome ...

, the user can train a

random forest Random forests or random decision forests is an ensemble learning method for statistical classification, classification, regression analysis, regression and other tasks that works by creating a multitude of decision tree learning, decision trees ...

classifier. Trained ilastik classifiers can be applied new data not included in the training set in ilastik via its batch processing functionality, or without using the graphical user interface, in headless mode. ilastik can be integrated into various related tools: * Pre-trained workflows can be executed directly from

ImageJ ImageJ is a Java (programming language), Java-based image processing program developed at the National Institutes of Health and the Laboratory for Optical and Computational Instrumentation (LOCI, University of Wisconsin). Its first version, ImageJ ...

Fiji Fiji, officially the Republic of Fiji, is an island country in Melanesia, part of Oceania in the South Pacific Ocean. It lies about north-northeast of New Zealand. Fiji consists of an archipelago of more than 330 islands—of which about ...

using the ilastik-ImageJ plugin. * Pre-trained ilastik Pixel Classification workflows can be run directly in

Python Python may refer to: Snakes * Pythonidae, a family of nonvenomous snakes found in Africa, Asia, and Australia ** ''Python'' (genus), a genus of Pythonidae found in Africa and Asia * Python (mythology), a mythical serpent Computing * Python (prog ...

with the ilastik Python package, which is available via conda. * ilastik has a

CellProfiler CellProfiler is free, open-source software designed to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically. Advanced algorithms for image analysis are av ...

module to use ilastik classifiers to process images within a

framework.

History

ilastik was first released in 2011 by scientists at the Heidelberg Collaboratory for Image Processing (HCI),

University of Heidelberg Heidelberg University, officially the Ruprecht Karl University of Heidelberg (; ), is a public university, public research university in Heidelberg, Baden-Württemberg, Germany. Founded in 1386 on instruction of Pope Urban VI, Heidelberg is List ...

Application

* The Interactive Learning and Segmentation Toolkit * Carving * Cell classification and neuron classification * Synapse detection * Cell tracking * Neural Network Classification

Resources

ilastik project is hosted on

GitHub GitHub () is a Proprietary software, proprietary developer platform that allows developers to create, store, manage, and share their code. It uses Git to provide distributed version control and GitHub itself provides access control, bug trackin ...

. It is a collaborative project, any contributions such as comments, bug reports, bug fixes or code contributions are welcome. The ilastik team can be contacted for user support on the image.sc forum.

References

External links

* *
ImageJ plugin on github

ilastik on forum.image.sc
{{Image_Processing_Software Image segmentation Computer vision software Data mining and machine learning software Free software programmed in Python