Data from: Viscosity voxel counts in mucus aggregates from diatom cultures and coastal samples
Abstract
This dataset contains microviscosity voxel counts, the spatial gradient of microviscosity voxel counts, bacteria counts, and other metadata for mucus aggregates imaged with confocal microscopy of the molecular rotor RY3 and SYBR Green I. There are 39 mucus aggregates analyzed from laboratory cultures of Chaetoceros affinis diatoms and 13 from coastal samples collected off the pier at Scripps Institution of Oceanography. Of the 39 C. affinis aggregates, 7 were imaged at 3 time points over ~7 hours. Confocal z-stacks were calibrated and analyzed using the ry3_analysis code available at the DOI 10.5281/zenodo.20800236. The microviscosity voxel counts are used to calculate microviscosity probabilities in close proximity to bacteria, in the aggregates, and in the seawater surrounding aggregates. Representative images, probability plots, and methodological details are available in the Supplementary Material of the associated manuscript (DOI 10.1126/science.adx4170).
Dataset DOI: 10.5061/dryad.x0k6djj26
Description of the data and file structure
The aggregate microviscosity and bacteria dataset is contained in the struct rc in the MATLAB data file rcd.mat. The microviscosities are relative to seawater and are reffered to as 'viscosity' herein.
Files and variables
File: rcd.mat
Description:
The variable rc contains the following 1x1 structs:
- m: General metadata.
- d: Data for the 32 single time point C. affinis aggregates.
- p: Data for the 13 aggregates collected from coastal samples.
- t: Data for the 7 C. affinis aggregates measured at 3 time points each.
Variables within these structs are detailed below. Aggregates in d and p use the naming convention eXX_mYYrZZ where XX is the experiment ID, YY is the sample ID, and ZZ is the optical configuration ID. Aggregates in t use the naming convention eXX_mYYrZZ_T where T is the time point.
Variables
- vbin (1x1000 double): The viscosity count bin centers. The bin widths are 0.1 relative viscosity units with a range of 0-100.
- gbin (1x200 double): The spatial gradient of viscosity count bin centers. The bins are 1 μm-1 wide with a range of 0-200 μm-1.
- dbin (1x100 double): The relative distance count bin centers. The distance of voxels inward from the boundary of an aggregate is relative to the maximum distance inside the aggregate. The bins are 0.01 relative distance units with a range of 0-1.
- eXX_mYYrZZ (1x1 struct): Data for each aggregate.
- v (1x1 struct): Vicscosity data.
- havc (1x1000 double): Viscosity counts within 0.3 μm of bacteria associated with the aggregate with bin centers vbin.
- hovc (1x1000 double): Viscosity counts within 0.3 μm of bacteria outside of the aggregate with bin centers vbin.
- ravc (1x1000 double): Viscosity counts within the aggregate with bin centers vbin.
- rovc (1x1000 double): Viscosity counts outside the aggregate with bin centers vbin.
- dvh (100x1000 double): Viscosity counts at relative distances near bacteria associated with the aggregate (bin centers dbin x vbin).
- dvr (100x1000 double): Viscosity counts at relative distances within the aggregate (bin centers dbin x vbin).
- g (1x1 struct): Viscosity gradient data.
- hagc (1x200 double): Viscosity gradient counts within 0.3 μm of bacteria associated with the aggregate with bin centers gbin.
- hogc (1x200 double): Viscosity gradient counts within 0.3 μm of bacteria outside of the aggregate with bin centers gbin.
- ragc (1x200 double): Viscosity gradient counts within the aggregate with bin centers gbin.
- rogc (1x200 double): Viscosity gradient counts outside the aggregate with bin centers gbin.
- m (1x1 struct): Metadata.
- vox (1x1 double): The voxel volume in μm3.
- avol (1x1 double): The aggregate volume in μm3.
- bvol (1x1 double): The bacterial volume in μm3.
- vmd (1x1 double): The median aggregate viscosity.
- bacounts (1xn double): The number of bacteria estimated per cluster (n).
- aggin (1xn logical): For each cluster in bacounts, true is aggregate-associated and false is outside the aggregate.
- v (1x1 struct): Vicscosity data.
- eXX_mYYrZZ (1x1 struct): Data for each aggregate.
- v (1x1 struct): Vicscosity data.
- havc, hovc, ravc, rovc: Same as above.
- g (1x1 struct): Viscosity gradient data.
- hagc, hogc, ragc, rogc: Same as above.
- m (1x1 struct): Metadata.
- vox, avol, bvol, vmd: Same as above.
- v (1x1 struct): Vicscosity data.
- eXX_mYYrZZ_T (1x1 struct): Data for each aggregate at each time point.
- v (1x1 struct): Vicscosity data.
- havc, hovc, ravc, rovc: Same as above.
- g (1x1 struct): Viscosity gradient data.
- hagc, hogc, ragc, rogc: Same as above.
- d (1x1 struct): Bacteria distance with respect to the aggregate data.
- db (nx1 double): The distance of bacterial clusters (n) from the centroid of the aggregate in μm.
- de (nx1 double): The distance of the aggregate boundary from the centroid of the aggregate in the direction of each cluster in db.
- baco (1xn double): The number of bacteria estimated per cluster in db.
- m (1x1 struct): Metadata.
- vox, avol, bvol, vmd: Same as above.
- tdur (1x1 double): For each time point, the time duration from the first time point in hours.
- v (1x1 struct): Vicscosity data.
Code/software
The file rcd.mat was generated in MATLAB R2024b and can be loaded with any version of MATLAB.