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ilastik specifications


Unique identifier OMICS_06488
Name ilastik
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes


No version available


  • person_outline ilastik Team

Publication for ilastik

ilastik citations


Concepts in Light Microscopy of Viruses

PMCID: 5923496
PMID: 29670029
DOI: 10.3390/v10040202

[…] tterns in a dataset. In a biomedical imaging context, ML is typically used for relatively simple tasks, such as segmentation, tracking, denoising, and phenotype determination. For example, tools like Ilastik [] and CellCognition provide easy-to-use and powerful ways to segment and classify of images by reinforced machine learning [].Recent advances in computing, specifically in graphical processin […]


MeioSeed: a CellProfiler based program to count fluorescent seeds for crossover frequency analysis in Arabidopsis thaliana

Plant Methods
PMCID: 5905130
PMID: 29692862
DOI: 10.1186/s13007-018-0298-3

[…] t program to count Arabidopsis seeds from fluorescence microscopy images. Using the meiotic reporter line Col3-4/20, we showed that MeioSeed accurately counts red and green fluorescent seeds using an Ilastik-based seed classifier with adjustable detection thresholds for fluorescence. Furthermore, we demonstrated the optimization of the fluorescence threshold settings to fit the known model for rec […]


Francisella tularensis D Ala D Ala Carboxypeptidase DacD Is Involved in Intracellular Replication and It Is Necessary for Bacterial Cell Wall Integrity

PMCID: 5903032
PMID: 29692981
DOI: 10.3389/fcimb.2018.00111
call_split See protocol

[…] f cell size differences, multiple random TEM images of wild-type and mutant cells taken at equal magnification of 11,000 x were used. Cell profiles were segmented using machine learning algorithms in ilastik software (Sommer et al., ), and areas determined in Fiji ImageJ (Schindelin et al., ). Total of 1,945 wild-type and 173 mutant cells were analyzed. Cell profiles exhibiting membrane defects we […]


Automated C. elegans embryo alignments reveal brain neuropil position invariance despite lax cell body placement

PLoS One
PMCID: 5874040
PMID: 29590193
DOI: 10.1371/journal.pone.0194861

[…] s subtracted from the green channel before analysis, to eliminate bleedthrough of the red channel, which was otherwise substantial.Green channel segmentation of cell bodies, neurites, and nuclei used Ilastik [], a random forest [] machine learning method that segments images based on a combination of classifiers such as raw intensity, Difference of Gaussians, and Laplacian of Gaussian. Segmentatio […]


Moderate Modulation of Cardiac PGC 1α Expression Partially Affects Age Associated Transcriptional Remodeling of the Heart

Front Physiol
PMCID: 5871735
PMID: 29618980
DOI: 10.3389/fphys.2018.00242

[…] 3 incubations with 100% ethanol, cleared in xylene and mounted with Histomount (Invitrogen). Quantification of the collagen amount from the Picrosirius Red staining was carried out with the software Ilastik 1.1 and Fiji. Briefly, 12 images representing the true staining (collagen = red; background = yellow) as well as artifacts such as dirt, wrinkles, blood, image noise, blood vessels, unevenness […]


Clathrin adaptor ratio and membrane tension regulate the flat to curved transition of the clathrin coat during endocytosis

Nat Commun
PMCID: 5856840
PMID: 29549258
DOI: 10.1038/s41467-018-03533-0

[…] For tracking CME events, we used ilastik ( First, the images were segmented using the pixel classification and object classification workflow. For tracking, the automatic tracking workflow was used. The maximal di […]


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