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LABKIT: Labeling and Segmentation Toolkit for Big Image Data

Arzt, Matthias, Deschamps, Joran, Schmied, Christopher, Pietzsch, Tobias, Schmidt, Deborah, Tomancak, Pavel, Haase, Robert, Jug, Florian·2022·Frontiers in Computer Science
DOI 10.3389/fcomp.2022.777728

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Abstract

We present LABKIT, a user-friendly Fiji plugin for the segmentation of microscopy image data. It offers easy to use manual and automated image segmentation routines that can be rapidly applied to single- and multi-channel images as well as to timelapse movies in 2D or 3D. LABKIT is specifically designed to work efficiently on big image data and enables users of consumer laptops to conveniently work with multiple-terabyte images. This efficiency is achieved by using ImgLib2 and BigDataViewer as well as a memory efficient and fast implementation of the random forest based pixel classification algorithm as the foundation of our software. Optionally we harness the power of graphics processing units (GPU) to gain additional runtime performance. LABKIT is easy to install on virtually all laptops and workstations. Additionally, LABKIT is compatible with high performance computing (HPC) clusters for distributed processing of big image data. The ability to use pixel classifiers trained in LABKIT via the ImageJ macro language enables our users to integrate this functionality as a processing step in automated image processing workflows. Finally, LABKIT comes with rich online resources such as tutorials and examples that will help users to familiarize themselves with available features and how to best use LABKIT in a number of practical real-world use-cases.

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Figures

Image 1
CC-BY · From the PDF
FIGURE 2 Semantic segmentation of microscopy images with LABKIT's pixel classification: (A) Maximum intensity projection of a confocal stack showing HeLa cells expressing C1-GFP (left), next to the sparse labeling (scribbles, center) and resulting cell segmentation (right). (B) Bright field microscopy image of E.coli , sparse labeling discriminating cells and background and the resulting segmentation. Arrowheads show that segmentation of out-of-focus objects can be reduced by including pixels of such objects in the background class. (C) Fixed mouse liver tissue section stained with immunofluorescence and imaged in multiple channels with a spinning disk confocal microscope, showing Hepatocyte nuclei stained with antibody against HNF-4 α a transcription factor expressed in hepatocytes, hepatocyte cytoplasm (autofluorescence) and all nuclei stained with DAPI. (D) Labeling and resulting segmentation of the liver tissue section shown in (A) , segmenting Hepatocyte cytoplasm (green), Hepatocyte nuclei (blue), nuclei of non-parenchymal cells (yellow) and sinusoids (magenta). Scale bars 20 µ m (A) , (C) , and 5 µ m (B) .
FIGURE 2 Semantic segmentation of microscopy images with LABKIT's pixel classification: (A) Maximum intensity projection of a confocal stack showing HeLa cells expressing C1-GFP (left), next to the sparse labeling (scribbles, center) and resulting cell segmentation (right). (B) Bright field microscopy image of E.coli , sparse labeling discriminating cells and background and the resulting segmentation. Arrowheads show that segmentation of out-of-focus objects can be reduced by including pixels of such objects in the background class. (C) Fixed mouse liver tissue section stained with immunofluorescence and imaged in multiple channels with a spinning disk confocal microscope, showing Hepatocyte nuclei stained with antibody against HNF-4 α a transcription factor expressed in hepatocytes, hepatocyte cytoplasm (autofluorescence) and all nuclei stained with DAPI. (D) Labeling and resulting segmentation of the liver tissue section shown in (A) , segmenting Hepatocyte cytoplasm (green), Hepatocyte nuclei (blue), nuclei of non-parenchymal cells (yellow) and sinusoids (magenta). Scale bars 20 µ m (A) , (C) , and 5 µ m (B) .CC-BY · From the PDF
FIGURE 3 LABKIT labeling tools used for curation: labels generated by manual dense labeling or automatic segmentation can be efficiently curated with drawing, filling, erasing, or deletion of entire objects. Scale bar 10 µ m.
FIGURE 3 LABKIT labeling tools used for curation: labels generated by manual dense labeling or automatic segmentation can be efficiently curated with drawing, filling, erasing, or deletion of entire objects. Scale bar 10 µ m.CC-BY · From the PDF
FIGURE 4 Comparing automatic and manual ground-truth generation with LABKIT: (A) Fluorescence image of nuclei (out of 26 images) extracted from the 2018 Data Science Bowl (Caicedo et al., 2019). (B) Results from LABKIT automated segmentation of (A) after extracting connected components and giving each instance a unique pixel value. The arrows point to various segmentation errors. On the top right corner, the total time necessary to obtain the corresponding segmentation of all 26 images (including labeling) is indicated. Below the timing is the average precision (see Methods) as compared to a dense manual labeling performed by another observer. (C) Curation of (B) with same post-processing. The arrows point to the corrected errors mentioned in (B) . The timing information includes (B) . (D) Dense manual labeling of (A) and the same post-processing as in (B) . No scale bar was available for the images.
FIGURE 4 Comparing automatic and manual ground-truth generation with LABKIT: (A) Fluorescence image of nuclei (out of 26 images) extracted from the 2018 Data Science Bowl (Caicedo et al., 2019). (B) Results from LABKIT automated segmentation of (A) after extracting connected components and giving each instance a unique pixel value. The arrows point to various segmentation errors. On the top right corner, the total time necessary to obtain the corresponding segmentation of all 26 images (including labeling) is indicated. Below the timing is the average precision (see Methods) as compared to a dense manual labeling performed by another observer. (C) Curation of (B) with same post-processing. The arrows point to the corrected errors mentioned in (B) . The timing information includes (B) . (D) Dense manual labeling of (A) and the same post-processing as in (B) . No scale bar was available for the images.CC-BY · From the PDF
FIGURE 5 Pixel classification failure modes: (A) Image of a contractile vacuole pore in paramecium caudatum acquired with transmission electron microscopy (left), in which inner pore (blue), cytoplasm (green) and background (magenta) were labeled with scribbles (center). LABKIT's classifier fails to distinguish background and inner pore classes (right). Image provided by Richard Allen (Cell Image Library, 38894). (B) Mitotic spindle of a Ptk2 cell expressing GFP-tubulin imaged in wide-field fluorescence (left). Left and right halves of the mitotic spindle are labeled in different classes (blue and green, respectively), while background is labeled in magenta (center). LABKIT's classifier is incapable of discriminating similar structures (right). Image provided by Sophie Dumont and Timothy J. Mitchison (Cell Image Library, 6568). (C) Bright field image of C. elegans (left), labeled with two classes (center): foreground (green) and background (magenta). After applying connected components analysis to the classification result, contiguous worms belong to the same object (right). Image provided by Fred Ausubel (Broad Bioimage Benchmark Collection, BBBC010). Scale bars (A) 500 nm, (B) 10 µ m, and (C) 500 µ m.
FIGURE 5 Pixel classification failure modes: (A) Image of a contractile vacuole pore in paramecium caudatum acquired with transmission electron microscopy (left), in which inner pore (blue), cytoplasm (green) and background (magenta) were labeled with scribbles (center). LABKIT's classifier fails to distinguish background and inner pore classes (right). Image provided by Richard Allen (Cell Image Library, 38894). (B) Mitotic spindle of a Ptk2 cell expressing GFP-tubulin imaged in wide-field fluorescence (left). Left and right halves of the mitotic spindle are labeled in different classes (blue and green, respectively), while background is labeled in magenta (center). LABKIT's classifier is incapable of discriminating similar structures (right). Image provided by Sophie Dumont and Timothy J. Mitchison (Cell Image Library, 6568). (C) Bright field image of C. elegans (left), labeled with two classes (center): foreground (green) and background (magenta). After applying connected components analysis to the classification result, contiguous worms belong to the same object (right). Image provided by Fred Ausubel (Broad Bioimage Benchmark Collection, BBBC010). Scale bars (A) 500 nm, (B) 10 µ m, and (C) 500 µ m.CC-BY · From the PDF
Image 6
CC-BY · From the PDF

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Citations

Cites

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Metadata

Authors
Arzt, M., Deschamps, J., Schmied, C., Pietzsch, T., Schmidt, D., Tomancak, P., Haase, R., & Jug, F.
Venue
Frontiers in Computer Science
Publisher
Frontiers Media SA
Published
2022-02-10
Volume
4
ISSN
2624-9898
DOI
10.3389/fcomp.2022.777728
Cited by
405
References
7
Licence
creativecommons.org/licenses/by/4.0/ (vor)
Funders
  • Max-Planck-Gesellschaft (M.IF.A.MOZG8106)
  • Bundesministerium für Bildung und Forschung (01IS18026C, 031L0102)
  • Deutsche Forschungsgemeinschaft (EXC2068, JU3110/1-1, TO563/8-1)
  • European Regional Development Fund (CZ.02.1.01/0.0/0.0/16_013/0001791)

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Arzt, M., Deschamps, J., Schmied, C., Pietzsch, T., Schmidt, D., Tomancak, P., Haase, R., & Jug, F. (2022). LABKIT: Labeling and Segmentation Toolkit for Big Image Data. Frontiers in Computer Science. https://doi.org/10.3389/fcomp.2022.777728