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. 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.

Node-RED

Node-RED is a programming tool for wiring together hardware devices, APIs and online services in new and interesting ways.

MorphoCut

MorphoCut is an image processing library designed to handle large volumes of biological, medical, oceanographic and remote sensing image data.

EcoTaxa

EcoTaxa is a web application dedicated to the visual exploration and the taxonomic annotation of images that illustrate the beauty of planktonic biodiversity.

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 acquired in fluidic mode. MorphoCut first applies a running median to approximate the background image based on 5 frames, a Canny Edge Detection via OpenCV is performed, followed by a dilation, closing and erosion functions also from OpenCV. From the binary image, MorphoCut extracts the vignette/ROI for each present object.

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 PlanktoScope is available on bioRvix :