Coral growth, retraction, defense, and regenerative strategies revealed by live microCT
Data files
Apr 16, 2026 version files 110.65 GB
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Fig1_Pocillopora_M1.zip
6.55 GB
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Fig1_Pocillopora_M2.zip
6.67 GB
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Fig1_Pocillopora_M3.zip
6.32 GB
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Fig1_Pocillopora_M4.zip
6.63 GB
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Fig2_Stylophora_M1.zip
5.21 GB
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Fig2_Stylophora_M5.zip
5.46 GB
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Fig3_Pocillopora_M1.zip
4.79 GB
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Fig3_Pocillopora_M2.zip
5.85 GB
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Fig3_Pocillopora_M3.zip
6.52 GB
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Fig3_Pocillopora_M4.zip
7.41 GB
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Fig4_Pocillopora_nanoCT.zip
13.13 GB
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Fig5_Pocillopora_M1.zip
4.90 GB
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Fig5_Pocillopora_M2.zip
6.24 GB
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Fig5_Pocillopora_M3.zip
11.57 GB
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Fig5_Pocillopora_M4.zip
11.19 GB
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Fig6_Stylophora_regeneration.zip
2.21 GB
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README.md
6.66 KB
Abstract
Understanding how corals build and remodel their skeletons is key to explaining reef resilience, yet most insights come from static imaging. Using longitudinal live microCT, we tracked the same coral colonies over weeks to months at micrometer resolution. Coral skeleton formation is not a uniform accretion process but a dynamic integration of multiple programs, including vertical and horizontal patterned growth, previously undescribed defensive wall-building against competitors, exploratory edge behavior with reversible expansions and retractions, and skeletal regeneration favoring rapid, imprecise yet effective matrix expansion. Time-resolved imaging links colony-scale growth to microscale events, showing that all modes depend on balances between fusion of skeletal granules and layered matrix deposition, guided by tissue pre-patterning. Beyond corals, this framework generalizes to studying skeletal dynamics across diverse biomineralizing organisms.
Dataset DOI: 10.5061/dryad.kh18932p4
Description of the data and file structure
This dataset contains tomographic slices obtained using X-ray micro-computed tomography (microCT). The scanned samples were living coral specimens of Pocillopora damicornis and Stylophora pistillata.
MicroCT measurements were performed at the Laboratory of X-ray Micro and Nano Computed Tomography (CTlab), Central European Institute of Technology, Brno University of Technology (CEITEC BUT). The instrument used was a GE v|tome|x L240 system equipped with a 180 kV / 15 W maximum power nanofocus X-ray tube and a high-contrast flat-panel detector (dynamic 41|100, 4000 × 4000 pixels, pixel size 100 × 100 μm).
The experimental geometry was configured to achieve a voxel resolution of 6 μm for both species. This resolution allowed the entire coral nubbin to remain within the field of view while enabling detection of small structural changes. The voxel resolution was kept constant throughout all longitudinal scans.
For the dataset provided here, the exposure time per projection was 334 ms, with 898 projections acquired per scan, resulting in a total scan time of approximately 5 minutes.
Files and variables
File: Fig1_Pocillopora_M1.zip
Description: Complex dynamics of coral growth captured by longitudinal microCT (a serie of tiff images, resolution 6 µm): Pocillopora damicornis - initial state.
File: Fig1_Pocillopora_M2.zip
Description: Complex dynamics of coral growth captured by longitudinal microCT (a serie of tiff images, resolution 6 µm): Pocillopora damicornis - initial state + 2 weeks.
File: Fig1_Pocillopora_M3.zip
Description: Complex dynamics of coral growth captured by longitudinal microCT (a serie of tiff images, resolution 6 µm): Pocillopora damicornis - initial state + 4 weeks.
File: Fig1_Pocillopora_M4.zip
Description: Complex dynamics of coral growth captured by longitudinal microCT (a serie of tiff images, resolution 6 µm): Pocillopora damicornis - initial state + 12 weeks.
File: Fig2_Stylophora_M1.zip
Description: Defensive growth modality of Stylophora pistillata (a serie of tiff images, resolution 6 µm): Initial state.
File: Fig2_Stylophora_M5.zip
Description: Defensive growth modality of Stylophora pistillata (a serie of tiff images, resolution 6 µm): Initial state + 5 weeks.
File: Fig3_Pocillopora_M1.zip
Description: Complex dynamics of coral growth involving horizonal expansion, retraction and regrowth (a serie of tiff images, resolution 6 µm): Pocillopora damicornis - initial state.
File: Fig3_Pocillopora_M2.zip
Description: Complex dynamics of coral growth involving horizonal expansion, retraction and regrowth (a serie of tiff images, resolution 6 µm): Pocillopora damicornis - initial state + 2 weeks.
File: Fig3_Pocillopora_M3.zip
Description: Complex dynamics of coral growth involving horizonal expansion, retraction and regrowth (a serie of tiff images, resolution 6 µm): Pocillopora damicornis - initial state + 4 weeks.
File: Fig3_Pocillopora_M4.zip
Description: Complex dynamics of coral growth involving horizonal expansion, retraction and regrowth (a serie of tiff images, resolution 6 µm): Pocillopora damicornis - initial state + 12 weeks.
File: Fig4_Pocillopora_nanoCT.zip
Description: Micro-level skeletal dynamics tracked in time by nanoCT (a serie of tiff images, resolution 1.47 µm): Pocillopora damicornis.
File: Fig5_Pocillopora_M1.zip
Description: Polyp formation in vertical growth (a serie of tiff images, resolution 6 µm): Pocillopora damicornis - initial state.
File: Fig5_Pocillopora_M2.zip
Description: Polyp formation in vertical growth (a serie of tiff images, resolution 6 µm): Pocillopora damicornis - initial state + 1 month.
File: Fig5_Pocillopora_M3.zip
Description: Polyp formation in vertical growth (a serie of tiff images, resolution 6 µm): Pocillopora damicornis - initial state + 3 months.
File: Fig5_Pocillopora_M4.zip
Description: Polyp formation in vertical growth (a serie of tiff images, resolution 6 µm): Pocillopora damicornis - initial state + 5 months.
File: Fig6_Stylophora_regeneration.zip
Description: Regenerative matrix allocation closes the chambers of dead polyps (a serie of tiff images, resolution 6 µm): Stylophora pistillata
Code/software
The microCT data are provided as a series of 16-bit grayscale tiff image stacks. Tiff is a standard, non-proprietary image format and can be opened using a wide range of free and open-source image processing software that supports 16-bit grayscale images.
The datasets can be viewed and processed using, for example:
- ImageJ/Fiji
- Other compatible software capable of reading 16-bit TIFF stacks (e.g., napari, 3D Slicer, or similar open-source tools)
- For data segmentation and analysis, we used the commercial software VGStudio MAX 2024.3 (Volume Graphics GmbH).
Workflow
Each dataset consists of sequential TIFF slices representing reconstructed MicroCT cross-sections. The images can be imported as an image sequence (stack) in ImageJ/Fiji using:
File → Import → Image Sequence
Once imported, the stack can be visualized, scrolled, and processed using standard 2D/3D tools within the software. No custom plugins, macros, or scripts are required to view the data.
Code and scripts
No custom code or scripts are required to open or visualize the data. All files are provided in a directly accessible format.
Access information
During this study, approximately 5 TB of microCT data was generated. Due to file size limitations and to ensure reasonable download accessibility, only representative datasets (corresponding to one specimen per Figure) are included in this DRYAD submission.
The deposited data are sufficient to reproduce the analyses and results presented in the manuscript.
Additional raw datasets are available from the corresponding author upon reasonable request.
Other publicly accessible locations of the data:
- The data are original and have not been previously published or deposited elsewhere. They are made publicly available through this DRYAD submission. The data were not derived from external sources.
Data was derived from the following sources:
- Not applicable. The data were generated by the authors and were not derived from external sources.