Published November 9, 2021
| Version v1
Dataset
Open
3D dataset of root soil bacteria dynamics obtained using large field of view light sheet microscope
Authors/Creators
- 1. University of Dundee
- 2. James Hutton Institute
- 3. The University of Sheffield
- 4. École Nationale Supérieure de Chimie de Montpellier
- 5. Scotland's Rural College
- 6. Ikerbasque
Description
A tailor made dual-illumination light-sheet system acquired photons scattered from the plant whilst fluorescence emissions were simultaneously captured from transparent soil particles and labelled microorganisms, allowing the generation of quantitative data on samples approximately 3600 mm3 in size with as good as 5 µm resolution at a rate of up to one scan every 30 minutes. The dataset shows the dynamics of Bacillus subtilis populations in the rhizosphere of lettuce plants in real time.
Notes
1 The dataset 'rawdata_Hourly_Scan_2019_05_24' is a time-lapse imaging of Bacillus subtilis populations in the rhizosphere of a lettuce plant with a rate of 60 minutes per volumetric scan. This dataset contains initial 12-hour raw images acquired from the camera and was processed and used in the SUPPLEMENTARY VIDEO 6, 7, and 8, Figure 4 and other analysis. In detail, the 'A' are root images from 633 nm scattering signal, the 'B' are transparent soil (Nafion) images from red fluorescence signal (excitation: 561nm, emission: longpass at 600 nm), and the 'D' are gfp-tagged Bacillus subtilis images from green fluorescence signal (excitation: 488 nm, emission: band-pass at 520 nm,36 nm band).
2 The dataset 'Hourly_Scan_2019_05_24' is the mat(MATLAB) file of the same scan but contains fully 23 hours. The image data in the mat file is affine transformed to real geometry and stiched into a whole 3D dataset. In detail:
'Root.mat' represents the timelapse dataset of the scattering signal intensity from which root length and position can be calculated
'Bacteria.mat' represents the timelapse dataset of the green fluorescence intensity from which bacterial cell density and position can be calculated
'Soil.mat' represents the timelapse dataset of the red fluorescence intensity from which the position of soil particles can be calculated
'stack_Distance_Pore' represents the sum of pixel as a function of the distance from root surface (D) and soil pore (P). D ranges from 0 to 3.6 mm and is decomposed into 128 intervals. P ranges from 0 to 0.8 mm and is decomposed into 128 intervals.
'stack_Distance_Pore_Intensity' represents the sum of pixel intensity as a function the distance from root surface (D) and soil pore (P). D ranges from 0 to 3.6 mm and is decomposed into 128 intervals. P ranges from 0 to 0.8 mm and is decomposed into 128 intervals.