Microplankton life histories revealed by holographic microscopy and deep learning
- Department of Physics, University of Gothenburg, Sweden
- Department of Marine Sciences, University of Gothenburg, Sweden
Figures
Figure 1 with 3 supplements
Experimental setup and deep-learning data analysis.
(a) Holographic microscope: Planktons suspended in a miniature sample well are imaged with an inline holographic microscope. The (cropped) example holographic image features two different plankton …
Figure 1—figure supplement 1
Holographic microscope and full-scale view of an experimental holographic image.
(a) Detailed view of the inline holographic microscope shown in Figure 1a: A plane wave generated by a monochromatic LED source illuminates the sample well that contains two different species of …
Figure 1—figure supplement 2
Simulated holographic images and RU-Net architecture.
(a) Examples of simulated plankton holograms generated by DeepTrack 2.0 (Midtvedt et al., 2021a): Each image () contains plankton holograms generated over a wide range of sizes and refractive …
Figure 1—figure supplement 3
Simulated plankton sequence and weighted-average convolutional neural network (WAC-Net) architecture.
(a) Simulated time sequence of holographic images cropped around an individual plankton: The 15-frame simulated sequence is an example input sequence for training the WAC-Net to estimate the …
Figure 2 with 1 supplement
Dry mass estimates.
(a) Phytoplankton species Oxyrrhis marina as detected by RU-Net on a portion of experimental hologram (see Figure 1—figure supplement 1 for the complete hologram). (b) Dry mass distributions for O. …
Figure 2—figure supplement 1
Dry mass and equivalent spherical radius (ESR) estimates for different species of planktons.
Comparison between dry mass (left panels) and ESR (right panels) estimated from volume-to-carbon relationships (Menden-Deuer and Lessard, 2000) (gray histograms) and dry mass estimated using our …
Figure 3 with 3 supplements
Feeding events.
3D recording of a feeding event where (a) a predator micro-zooplankton (Oxyrrhis marina, orange traces) approaches a prey phytoplankton (Dunaliella tertiolecta, blue traces), (b) feeds on it, and …
Figure 3—figure supplement 1
2D projection of traces in a feeding event.
2D recording of a feeding event where (a) a predator micro-zooplankton (Oxyrrhis marina, orange traces) approaches a prey phytoplankton (Dunaliella tertiolecta, blue traces), (b) feeds on it, and …
Figure 3—figure supplement 2
Feeding event main.
Figure 3—figure supplement 3
Feeding event additional.
(a–c) Snapshots of video (Video 2) showcasing an additional feeding event.
Figure 4 with 1 supplement
Growth and cell division of a diatom.
Different life stages of a diatom (Thallasiosira weissflogii) and its daughter cells: (a) the parent cell (blue), (b) divides into two daughter cells (orange); (c) the daughter cells continue to …
Figure 4—figure supplement 1
Division event.
Videos
Video 1
Feeding event 1.
Video 2
Feeding event 2.
Video 3
Division event.
Tables
Table 1
Planktons used in the experiments.
Strain identifier denotes strain code in Gothenburg University Marine Algae Culture Collection (GUMACC) and synonym strain identifier in parenthesis. The Oxyrrhis marina culture was kindly provided …
| Scientific name | Strain identifier | Class | ESD (mean ± SD) |
|---|---|---|---|
| Alexandrium minutum | GUMACC83 (CCMP113) | Dinophyceae | 18.3 ± 2.5 μm |
| Dunaliella tertiolecta | GUMACC5 | Cholorphceae | 6.7 ± 0.9 μm |
| Isochrysis galbana | GUMACC108 (CCMP1323) | Prymnesiophyceae | 4.0 ± 0.7 μm |
| Kryptoperidinium triquetrum | GUMACC71 (LAC20, KA86) | Dinophyceae | 14.9 ± 1.2 μm |
| Oxyrrhis marina | DTU-Aqua | Dinophyceae | 14.5 ± 1.5 μm |
| Rhodomonas salina | GUMACC126 (CCAP978/27) | Cryptophyceae | 7.4 ± 1.0 μm |
| Scripsiella acuminata | GUMACC110 (CCMP1331) | Dinophyceae | 17.7 ± 4.9 μm |
| Thallassiosira pseudonana | GUMACC132 (CCAP1085/12) | Cosconodiscophyceae | 4.8 ± 0.9 μm |
| Thallassiosira (Conticribra) weissflogii | GUMACC162 (CCAP1085/18) | Cosconodiscophyceae | 12.9 ± 1.4 μm |
