How it works

Overview

The PlanktoScope is an affordable, compact, digital microscope made of different simple modules.

The computing module is made of the latest Raspberry Pi 4 (4GB of LPDDR4 SDRAM) coupled with its Pi Camera (v2.1 - 8 megapixels). The optic is simplified using two reversed M12 lenses, the tube lens is fixed when the objective lens can be swapped offering a variety of optical configuration (Table 1). A motorized stage (~30 µm/step) allows a fine focus calibration of the swappable stage on which it’s possible to mount either µ-Slide I Luer or traditional glass slide depending on the mode (fluidic or static observation). A peristaltic pump driven by a stepper motor owning an order of precision ~ 0.1ml/min is used to drag the fluid into the flow-cell if needed.

Software Architecture

The Raspberry Pi is able to generate a standalone WiFi enabling the access of a web interface from a variety of devices (smartphone, tablet and laptop). The web interface is powered with node-RED offering both front and back end access. The GUI accessible on the front-end enable the acquisition of standardized raw images along with metadata which are perfect input for a python pipeline using MorphoCut and then EcoTaxa.

Image processing pipeline

Workflow used to segment the objects imaged in a frame and to extract features. Several operations are applied on the raw images (1) acquired in fluidic mode. MorphoCut first applies a running median to approximate the background image (2) based on 5 frames, a Canny Edge Detection via OpenCV is performed, followed by a dilation, closing and erosion functions (3) also from OpenCV. From the binary image, MorphoCut extracts the vignette/ROI for each present object (4).

Image a culture

Non-destructive continuous monitoring of lab cultures using a PlanktoScope allows for cell state to be measured at single cell resolution. A) Coscinodiscus wailesii cultures were monitored over a period of 6 hours. Creating a simple montage allows the user to easily quantify living or dead cells at different time points. B) Pyrocystis noctiluca cultures were monitored over a period of 6 hours during their conditioned night to day transition. Dividing cells are easily identifiable.

Image an environmental sample

1: Trichodesmium, 2: Copepoda, 3: Nauplii, 4: Egg, 5: Rhabdonella, 6: Cyttarocylis, 7: Undellidae, 8: Codonaria, 9: Ciliophora, 10: Codonellopsis, 11: Dictyocysta, 12: Chaetoceros, 13: Asterionellopsis, 14: Bacteriastrum, 15: Pennate chain, 16: Licmophora, 17: Licmophora, 18: Striatella, 19: Rhizosolenia, 20: Coscinodiscophyceae, 21: Bacillariophyceae, 22: Guinardia, 23: Dictyochophyceae, 24: Acantharea, 25: Rhizaria, 26: Rhizaria, 27: Acantharea, 28: Acantharea, 29: Foraminifera, 30: Peridinales, 31: Pyrocystis, 32: Neoceratium, 33: Neoceratium ranipes, 34: Neoceratium, 35: Neoceratium fusus, 36: Neoceratium furca, 37: Dinophyceae, 38: Neoceratium pentagonum, 39: Protoperidinium, 40: Protoperidinium, 41: Dinophysis caudata, 42: Ornithocercus quadratus, 43: Ceratocorys

A preprint of the project is available on bioRvix :