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Endrov: an integrated platform for image analysis

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Figure 1: Screenshots of Endrov with sample data.

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Acknowledgements

We thank J. Koch, L. Meng, Z. Zhao, S. Le Guyader and R. Figueroa for ideas and feedback. We are grateful to C. Grove, P. Sternberg and WormBase for use of the Virtual Worm model (Howard Hughes Medical Institute and California Institute of Technology). This research was supported by the Swedish Research Council, Stiftelsen för Strategisk Forskning and the Center for Biosciences at Karolinska Institutet.

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Correspondence to Thomas R Bürglin.

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Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–4, Supplementary Tables 1 and 2 and Supplementary Methods (PDF 1200 kb)

Supplementary Software

Endrov (ZIP 132726 kb)

Supplementary Data 1

Estimation of dynamic range expansion. Exposure times and maximal intensity of selected frames from the recording BC15177_070605.ost. The average background signal on the slide outside the embryo was 40.4 ± 0.92 (s.d.), and the average signal background of the embryo itself (slight autofluorescence) was 56.3 ± 2.3 (s.d.). By fluctuating the exposure time from 180 ms to 15 ms, we achieved a dynamic range expansion of about a factor of 10. (XLS 98 kb)

Supplementary Data 2

Embryo data set with ceh-37. ceh-37::GFP expression data, mapped to the lineage. Unzip and load into Endrov to visualize and view on the 4D model and the lineage viewer. This data set includes only the annotated cells in this recording. Viewing this or any other expression pattern on the entire model requires an embryonic model, e.g., Ce2008. (ZIP 59 kb)

Supplementary Data 3

The C. elegans 2008 model of embryogenesis. The Ce2008 embryonic model is provided for viewing of ceh-37 and other expression data (previously published in Hench, J., Henriksson, J., Lüppert, M. & Bürglin, T.R. Dev. Biol. 333, 1–13 (2009)). Unzip before loading into Endrov. (ZIP 3329 kb)

Supplementary Data 4

Adult data set. Data of the adult cell outlines imported from http://caltech.wormbase.org/virtualworm/, by C. Grove. Unzip before loading into Endrov. (ZIP 4840 kb)

Example of 2D manual lineaging (video 1 of 3)

Example of the process of annotating an embryo, recorded with differential interference contrast microscopy, and how to combine the 2D, 3D and lineage viewers. (MOV 26508 kb)

Example of 3D manual lineaging (video 2 of 3)

This shows how to improve the coordinates of cells when, for example, a histone::RFP marker has been recorded. (MOV 16847 kb)

Example of how to generate a view of the adult 3D model (video 3 of 3)

In this video, the adult model is used to highlight the identity and location of descendant cells from the embryo. (MOV 19717 kb)

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Henriksson, J., Hench, J., Tong, Y. et al. Endrov: an integrated platform for image analysis. Nat Methods 10, 454–456 (2013). https://doi.org/10.1038/nmeth.2478

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