ilastik protocols

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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


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Publication for ilastik

ilastik in pipelines

PMCID: 5096676
PMID: 27814364
DOI: 10.1371/journal.pcbi.1005177

[…] (primarily using thresholding, watershed transform, and voronoi algorithms). supervised machine learning methods have also seen significant success in this space [–]. two notable examples are ilastik and microscopy image browser, two freely available programs that use supervised machine learning (edge and texture filters with random forest classification) to perform segmentation [, –]., […]

PMCID: 5096676
PMID: 27814364
DOI: 10.1371/journal.pcbi.1005177

[…] combinations of these standard techniques to solve the image segmentation problem for specific experiments, there is a barrier to sharing work and ideas in this space. cellprofiler, oufti, and ilastik represent notable exceptions, and have empowered a number of experiments, including in labs which were otherwise new to computational image analysis [, , ]. however, the overall lack […]

PMCID: 5134023
PMID: 28334699
DOI: 10.1098/rsif.2016.0725

[…] track cells in epithelial tissues []., software implementations and computational tools for cell tracking include farsight [] (segmentation only), seedwatersegmenter [] (nearest-neighbour tracking), ilastik [] (chain-graph models), tufts tissue tracker [] (min-cost max-flow algorithm), tracking with gaussian mixture models [] (nearest-neighbour tracking), packing analyzer [] (particle image […]

PMCID: 4448323
PMID: 26022740
DOI: 10.1186/s12859-015-0618-9

[…] they are available either as generic frameworks (such as weka [] or knime []) or integrated into bioanalysis tools (such as pslid/slic [], cellprofiler [], wndchrm [], cellexplorer [], ilastik [] or biocat []), please see [] for an overview., this section evaluates the goodness of the classification achieved using the proposed feature set and the decision tree classifier. […]

PMCID: 4659165
PMID: 26607933
DOI: 10.1186/s12859-015-0814-7

[…] default parameters and with hand-adjusted parameters, and report best results; scoring of the exported segmentations required ad-hoc removal of segment borders and anti-aliasing artifacts. we ran ilastik v1.1 with hysteresis thresholding (low and high set to 0.20 and 0.80, respectively), using ~230 brush strokes to provide examples of background and foreground pixels, and tried a number […]

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ilastik in publications

PMCID: 5923496
PMID: 29670029
DOI: 10.3390/v10040202

[…] 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 […]

PMCID: 5902610
PMID: 29662076
DOI: 10.1038/s41467-018-03571-8

[…] nine field of view for each well and three different fluorescent channels (gfp, cy5 and dapi) per position., the image and data analysis was performed using the open-source software packages ilastik, cellprofiler and r ( to analyse phalloidin images and distinguish between pixels that belong to cdrs from other actin-rich structures such as stress fibres, […]

PMCID: 5903032
PMID: 29692981
DOI: 10.3389/fcimb.2018.00111

[…] 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 […]

PMCID: 5902527
PMID: 29692722
DOI: 10.3389/fphar.2018.00178

[…] immuno research)., subsequently, the total area of lung was scanned with a bx51 microscope equipped with the virtual microscopy system dotslide (olympus, japan) and subjected to segmentation in ilastik software to assess the relative cd31 immunopositive area to the all-tissue area. image segmentation was performed in ilastik (developed by the ilastik team, with partial financial support […]

PMCID: 5915156
PMID: 29707148
DOI: 10.18632/oncotarget.24891

[…] blood vessels, as reported previously []. all images were scanned with a bx51 microscope equipped with virtual microscopy system dotslide (olympus, japan). image segmentation was performed using ilastik (developed by the ilastik team, with partial financial support by the heidelberg collaboratory for image processing, hhmi janelia farm research campus and cellnetworks excellence cluster)., […]

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