Flowcharts of automatic image acquisition and cell enumeration pipeline (Fig. S1); flowcharts of sequential z-stack, quick-stack, and focused quick-stack image acquisition for extended depth-of-field calculation (Fig. S2); grayscale micrographs showing autofluorescence signals detected in the channel for FISH signals as well as the channel for autofluorescence signals (Fig. S3); grayscale micrographs of small and large phytoplankton cells (Fig. S4); grayscale micrographs showing cell debris (Fig. S5); grayscale micrographs showing small and large phytoplankton, cell debris, and out-of-focus areas (Fig. S6); on-board performance test of three different methods for stack image acquisition with extended depth-of-focus calculation (Table S1).
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