(a) e-HCFM workflow applied to Tara Oceans samples: (1) 72 nano-plankton (size range 5–20 μm) samples collected during the Tara Oceans expedition (Pesant et al., 2015) were fixed in …
This image acquisition registry details the e-HCFM imaging runs, their metadata, their samples of origin, and associated metadata from the Tara Oceans expedition.
List of descriptors computed for each object imaged through e-HCFM.
The samples (Tara Oceans expeditions) were fixed on board with a PFA-Glutaraldehyde buffer. They have been kept at 4°C for several years. The specimens were imaged manually from regular e-HCFM …
Four fluorescent channels were recorded: (i) Green, cellular membranes (DiOC6(3)) indicates the core cell bodies and organelles; (ii) Blue, DNA (Hoechst) is used to localize DNA and the nuclei; …
(a) Sample preparation scheme (<1 hr). Concentrated cells from plankton samples are loaded into an eight-chamber Lab-TekTM II (Nunc 155382, Thermo Fisher Scientific, MA, USA) slide coated with …
(a) Overlapping field of view (fov) reduces detection biases of large planktonic particles. The percentage of overlap between fovs is defined to fit the highest expected cell size. To avoid …
Alexa-PLL staining clearly improved the full detection of almost all cells and specifically of their extensions and transparent biomineral structures (e.g. diatoms). The staining intensity is …
Each column represents one acquisition (in chronological order; acquisition spans a 10-month period) and the y-axis indicates the intensity value of voxels inside the bead (the data for each …
Bead intensities for each bead.
This is the source data for Figure 1— figure supplement 6.
The specimen (surface water, Tara Ocean station 72) was imaged manually from regular e-HCFM sample preparation with a Leica SP8 confocal laser scanning microscope (40X NA1.1 water). Four fluorescent …
These seven cells, fixed on board Tara and kept at 4°C for several years, were imaged manually using the e-HCFM workflow (Figure 1). Each cell is illustrated by two panels: the left side overlays …
The two first rows of the plate illustrate how the epiphytic nano-flagellate cells are attached on the diatom frustule. They live in small tubes (lorica) which are bound at the base of the setae …
The specimen (surface water, Tara Ocean station 137) was imaged manually from regular e-HCFM sample preparation with a Leica SP8 confocal laser scanning microscope (40X NA1.1 water). Four …
(a) Overview of the training set as a hierarchical pie chart. The size of the slices scales with the number of elements in the training set (details in Figure 3—source data 1). Accuracy values (%) …
Organization of the hierarchical classification scheme for the automated classification, the training set categories abundance and the recall value for each category of the four levels (four tables).
Confusion matrix generated by the classifier at the classification level 4.
Relative abundance of each taxon in each sample.
The relationship between sample label and sampling location is provided in ‘Figure 1—source data 1.’.
Assignment of stations to oceanic provinces.
Object counts (normalized to seawater volume) per taxonomic group (panel d).
Measured PO₄ concentrations (panel d).
Values of N, Spearman correlation (rho), and number of samples (N) for each sub-group (panel d).
Both rows and columns represent the 155 categories. Cells are filled in whenever there is at least one labeled object of the category indicated in the row classified into the category indicated by …
Shows the accuracy as a function of the fraction of high-confidence objects that are kept, results are displayed at the most-detailed, fourth level (left, 155 categories) or the intermediate third …
Classification results for all objects in the training data at the fourth (finest) resolution level presented in in left panel (obtained by cross-validation).
Classification results for all objects in the training data at the third resolution level presented in right panel (obtained by cross-validation).
Principal component analysis of relative abundances of living single cells. Colors indicate ocean basin (IO: Indian Ocean, SAO: South Atlantic Ocean, SO: Southern Ocean, SPO: South Pacific Ocean, …
Derived principal component values (original data is Figure 3—source data 2).
Accuracy was estimated by cross-validation, using a feature selection step prior to classification. Source data are available in the file Figure 3—figure supplement 4—source data 1.
Accuracy of classification (estimated by cross validation) using a limited number of features (from 5 to 480, in increments of 5).