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ilastik  (Oxford Instruments)


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    Oxford Instruments ilastik
    Ilastik, supplied by Oxford Instruments, used in various techniques. Bioz Stars score: 99/100, based on 44673 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/ilastik/Imaris/pm42826711-58-9-11
    Average 99 stars, based on 44673 article reviews
    ilastik - by Bioz Stars, 2026-11
    99/100 stars

    Images

    Related Articles

    Confocal Microscopy:

    Article Title: Protocol for the three-dimensional analysis of rodent skeletal muscle.
    Article Snippet: Confocal imaging is a powerful tool capable of analyzing cellular spatial data within a given tissue.. Here, we present a protocol for preparing optically cleared extensor digitorum longus (EDL) skeletal muscle samples suitable for confocal imaging/computational analysis.. We describe steps for sample preparation (including perfusion fixation and tissue clearing of muscle samples), image acquisition, and computational analysis, with sample segmentation/3D rendering outlined.

    Software:

    Article Title: Protocol for the three-dimensional analysis of rodent skeletal muscle.
    Article Snippet: Confocal imaging is a powerful tool capable of analyzing cellular spatial data within a given tissue.. Here, we present a protocol for preparing optically cleared extensor digitorum longus (EDL) skeletal muscle samples suitable for confocal imaging/computational analysis.. We describe steps for sample preparation (including perfusion fixation and tissue clearing of muscle samples), image acquisition, and computational analysis, with sample segmentation/3D rendering outlined.

    other:

    Article Title: Protein domain characterization reveals human MIC60 tolerates loss of helical bundle domain
    Article Snippet: The FIBSEM stack and prediction outputs from Ilastik were loaded to Imaris (v10.2.0) to clean up the segmentation, analyze the mitochondrial volume, and generate the final images and videos.



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    Image Search Results


    Combined Ilastik®, ImageJ, and Imaris® processing pipeline. A) Individual z-slices were selected from the 3D LSM image that represented the inter-condition, inter-replicate, and intra-sample variability. The Ilastik® classifier was trained to select “nerve” and “not nerve” or background data. Post-training, Ilastik® segmentation was applied to all the z-slices in each 3D image. Samples were then processed in ImageJ to generate binary nerve masks. Binary nerve masks were imported back into Imaris® for 3D segmentation, and re-masking for statistical analyses. B) Comparison of Imaris® intensity-based segmentation and 3D reconstruction with Ilastik® machine learning segmentation and Imaris® 3D reconstruction. Scale bar = 100 μm. C) Comparison of Ilastik® machine learning segmentation with one, two, or four training slices. One and two training slices were intra-sample slices, while four slices combined two sets of intra-sample slices from two independent replicates. Scale bar = 100 μm.

    Journal: Bone Reports

    Article Title: A novel workflow for 3D imaging and spatial analysis of nerves in bone ☆

    doi: 10.1016/j.bonr.2025.101881

    Figure Lengend Snippet: Combined Ilastik®, ImageJ, and Imaris® processing pipeline. A) Individual z-slices were selected from the 3D LSM image that represented the inter-condition, inter-replicate, and intra-sample variability. The Ilastik® classifier was trained to select “nerve” and “not nerve” or background data. Post-training, Ilastik® segmentation was applied to all the z-slices in each 3D image. Samples were then processed in ImageJ to generate binary nerve masks. Binary nerve masks were imported back into Imaris® for 3D segmentation, and re-masking for statistical analyses. B) Comparison of Imaris® intensity-based segmentation and 3D reconstruction with Ilastik® machine learning segmentation and Imaris® 3D reconstruction. Scale bar = 100 μm. C) Comparison of Ilastik® machine learning segmentation with one, two, or four training slices. One and two training slices were intra-sample slices, while four slices combined two sets of intra-sample slices from two independent replicates. Scale bar = 100 μm.

    Article Snippet: Comparing the Ilastik® pipeline with Imaris® intensity-based segmentation, we demonstrated improved segmentation of nerve-like structures, with reduced segmentation of non-nerve background ( B).

    Techniques: Comparison

    Whole mount calvarial defect nerve image processing and analysis. A) Maximum intensity projection (MIP) image of TUBB3+ nerves in the calvarial defects 1 week, 2 weeks, and 4 weeks after 4-mm critical-sized calvarial defect injury. B) Binary Ilastik® masks prior to ImageJ processing. C) Imaris® absolute segmentation used for nerve masking. D) Resulting nerve mask in Imaris®. E) Radial density plots for the calvarial defect at 1 week, 2 week, 4 weeks, and 8 weeks post-injury. Color bar indicates the 2D nerve density (μm 3 /μm 3 ) per radial region. Scale bar = 300 μm.

    Journal: Bone Reports

    Article Title: A novel workflow for 3D imaging and spatial analysis of nerves in bone ☆

    doi: 10.1016/j.bonr.2025.101881

    Figure Lengend Snippet: Whole mount calvarial defect nerve image processing and analysis. A) Maximum intensity projection (MIP) image of TUBB3+ nerves in the calvarial defects 1 week, 2 weeks, and 4 weeks after 4-mm critical-sized calvarial defect injury. B) Binary Ilastik® masks prior to ImageJ processing. C) Imaris® absolute segmentation used for nerve masking. D) Resulting nerve mask in Imaris®. E) Radial density plots for the calvarial defect at 1 week, 2 week, 4 weeks, and 8 weeks post-injury. Color bar indicates the 2D nerve density (μm 3 /μm 3 ) per radial region. Scale bar = 300 μm.

    Article Snippet: Comparing the Ilastik® pipeline with Imaris® intensity-based segmentation, we demonstrated improved segmentation of nerve-like structures, with reduced segmentation of non-nerve background ( B).

    Techniques:

    Gold standard evaluation. A) Gold standard and Ilastik® overlay on TUBB3+, VAChT+, and Baf53b + nerves in calvarial defects, metatarsal bones, and knee joints, respectively. Scale bar is 100 μm. B) Percent overlap calculation, between gold standard and Ilastik® data.

    Journal: Bone Reports

    Article Title: A novel workflow for 3D imaging and spatial analysis of nerves in bone ☆

    doi: 10.1016/j.bonr.2025.101881

    Figure Lengend Snippet: Gold standard evaluation. A) Gold standard and Ilastik® overlay on TUBB3+, VAChT+, and Baf53b + nerves in calvarial defects, metatarsal bones, and knee joints, respectively. Scale bar is 100 μm. B) Percent overlap calculation, between gold standard and Ilastik® data.

    Article Snippet: Comparing the Ilastik® pipeline with Imaris® intensity-based segmentation, we demonstrated improved segmentation of nerve-like structures, with reduced segmentation of non-nerve background ( B).

    Techniques: