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# Funding
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The PlanktoScope project has been made possible by the generous support of a number of funders:
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# Disposal and recycling
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## The Raspberry PI
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The Raspberry Pi is a small computer developed by the Raspberry Pi Foundation, a UK-based charity. It is designed to be a low-cost and low-power device that can be used for a variety of purposes, including education, home automation, and prototyping.
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The supply chain for the Raspberry Pi involves a number of different stages, including sourcing raw materials, manufacturing, packaging, and distribution. Some of the materials used in the production of the Raspberry Pi include plastic, metal, and electronic components such as chips and sensors.
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|
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The manufacturing of the Raspberry Pi takes place at a factory in South Wales, UK. The factory is owned by a contract manufacturer called Sony UK Technology Centre, which is responsible for assembling the devices according to the specifications provided by the Raspberry Pi Foundation. Working conditions at the factory are reported to be good, with the company offering a range of benefits to its employees, including flexible working hours and a subsidised canteen.
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It is difficult to determine the exact amount of CO2 used in the production and transport of the Raspberry Pi, as it depends on a number of factors such as the distance the devices need to be shipped and the mode of transport used. However, the Raspberry Pi Foundation has stated that it is committed to reducing its carbon footprint and has implemented a number of measures to help achieve this, including the use of recycled materials and the optimization of its supply chain to minimize the need for transportation.
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The Raspberry Pi is designed to be easily recyclable, with the majority of its components able to be separated and recycled. The foundation recommends that users recycle their old Raspberry Pis through their local e-waste recycling program or a company that specializes in recycling electronic devices. It is difficult to determine the amount of waste produced during the disposal of the Raspberry Pi, as it depends on the specific recycling process used. However, recycling electronic devices can help to reduce the amount of waste that ends up in landfills and can also help to conserve valuable resources.
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# Supply chain report
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## The Raspberry PI
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The Raspberry Pi is a small computer developed by the Raspberry Pi Foundation, a UK-based charity. It is designed to be a low-cost and low-power device that can be used for a variety of purposes, including education, home automation, and prototyping.
|
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|
||||
The supply chain for the Raspberry Pi involves a number of different stages, including sourcing raw materials, manufacturing, packaging, and distribution. Some of the materials used in the production of the Raspberry Pi include plastic, metal, and electronic components such as chips and sensors.
|
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|
||||
The manufacturing of the Raspberry Pi takes place at a factory in South Wales, UK. The factory is owned by a contract manufacturer called Sony UK Technology Centre, which is responsible for assembling the devices according to the specifications provided by the Raspberry Pi Foundation. Working conditions at the factory are reported to be good, with the company offering a range of benefits to its employees, including flexible working hours and a subsidised canteen.
|
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|
||||
It is difficult to determine the exact amount of CO2 used in the production and transport of the Raspberry Pi, as it depends on a number of factors such as the distance the devices need to be shipped and the mode of transport used. However, the Raspberry Pi Foundation has stated that it is committed to reducing its carbon footprint and has implemented a number of measures to help achieve this, including the use of recycled materials and the optimization of its supply chain to minimize the need for transportation.
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The Raspberry Pi is designed to be easily recyclable, with the majority of its components able to be separated and recycled. The foundation recommends that users recycle their old Raspberry Pis through their local e-waste recycling program or a company that specializes in recycling electronic devices. It is difficult to determine the amount of waste produced during the disposal of the Raspberry Pi, as it depends on the specific recycling process used. However, recycling electronic devices can help to reduce the amount of waste that ends up in landfills and can also help to conserve valuable resources.
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<https://www.bmas.de/DE/Service/Gesetze-und-Gesetzesvorhaben/Gesetz-Unternehmerische-Sorgfaltspflichten-Lieferketten/gesetz-unternehmerische-sorgfaltspflichten-lieferketten.html>
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<https://www.csr-in-deutschland.de/DE/Wirtschaft-Menschenrechte/Gesetz-ueber-die-unternehmerischen-Sorgfaltspflichten-in-Lieferketten/gesetz-ueber-die-unternehmerischen-sorgfaltspflichten-in-lieferketten.html>
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<https://de.wikipedia.org/wiki/Lieferkettengesetz>
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Die Sorgfaltspflichten der Unternehmen erstrecken sich auf die gesamte Lieferkette – vom Rohstoff bis zum fertigen Verkaufsprodukt.
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Die Anforderungen an die Unternehmen sind nach den unterschiedlichen Stufen in der Lieferkette abgestuft:
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eigener Geschäftsbereich,
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unmittelbarer Zulieferer,
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mittelbarer Zulieferer.
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Und nach:
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Art und Umfang der Geschäftstätigkeit,
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dem Einflussvermögen des Unternehmens auf den Verursacher der Verletzung,
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der typischerweise zu erwartenden Schwere der Verletzung,
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der Art des Verursachungsbeitrags des Unternehmens.
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Die Anforderungen sind nach dem Einflussvermögen der Unternehmen in der Lieferkette abgestuft.
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Unternehmen müssen sowohl im eigenen Geschäftsbereich als auch beim unmittelbaren
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Zulieferer folgende Maßnahmen umsetzen:
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Grundsatzerklärung zur Achtung der Menschenrechte verabschieden.
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Risikoanalyse: Verfahren zur Ermittlung nachteiliger Auswirkungen auf die Menschenrechte durchführen.
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Risikomanagement (inklusive Präventions- und Abhilfemaßnahmen) zur Abwendung potenziell negativer Auswirkungen auf die Menschenrechte
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Beschwerdemechanismus einrichten.
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Transparent öffentlich Bericht erstatten.
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Im eigenen Geschäftsbereich müssen Unternehmen im Fall einer Verletzung im Inland unverzüglich Abhilfemaßnahmen ergreifen, die zwingend zur Beendigung der Verletzung führen.
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Beim unmittelbaren Zulieferer muss das Unternehmen einen konkreten Plan zur Minimierung und Vermeidung erstellen, wenn es die Verletzung nicht in absehbarer Zeit beenden kann.
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Bei mittelbaren Zulieferern:
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Hier gelten die Sorgfaltspflichten nur anlassbezogen und nur wenn das Unternehmen Kenntnis von einem möglichen Verstoß erlangt.
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In dem Fall hat das Unternehmen unverzüglich:
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Eine Risikoanalyse durchzuführen.
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Ein Konzept zur Minimierung und Vermeidung umsetzen.
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Angemessene Präventionsmaßnahmen gegenüber dem Verursacher zu verankern. Die Umsetzung von Brancheninitiativen ist hierbei eine Möglichkeit.
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Das Gesetz gilt auch für Zweigniederlassungen ausländischer Unternehmen in Deutschland, wenn sie insgesamt mehr als 3.000 Mitarbeitende (ab 2023) beziehungsweise 1.000 Mitarbeitende (ab 2024) in Deutschland beschäftigen.
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Der Geschäftsbereich deutscher Unternehmen wird erweitert: Kontrollierte Tochterunternehmen im Ausland werden zum eigenen Geschäftsbereich gerechnet und gelten nicht als erster Zulieferer.
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Ein weiteres Umweltabkommen, das Basler Abkommen zu Abfallexporten, wurde ergänzt. Dieses dient auch dem Schutz der menschlichen Gesundheit.
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Beim mittelbaren Zulieferer gelten Brancheninitiativen als angemessene Präventionsmaßnahme.
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Betriebsräte müssen über die Umsetzung des Gesetzes informiert werden.
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Klarstellung: Eine Verletzung der Pflichten aus diesem Gesetz begründet keine zivilrechtliche Haftung. Eine unabhängig von diesem Gesetz begründete zivilrechtliche Haftung bleibt unberührt.
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Klarstellung: Wenn ein Produktionsland internationale Abkommen nicht ratifiziert hat, ist das per se kein Grund, die Geschäftsbeziehungen in dieses Land abzubrechen.
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Ein neuer Titel: Lieferkettensorgfaltspflichtengesetz (LkSG).
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- The total number of suppliers and sites in your supply chain, and how they are distributed around the world
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- Non-compliances by country and type
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- Worker type analysis ie agency workers that represent a vulnerable group
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- Gender breakdown, and issues that disproportionately affect men and women
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- Suppliers at risk of lapsing their Sedex membership
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- When suppliers are due for an audit
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- <https://www.apics.org/docs/default-source/toc-pdfs/strategy-report-short.pdf>
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- <https://sscs.mit.edu/wp-content/uploads/2022/07/MIT-CTL-State-Supply-Chain-Sustainability-2022.pdf>
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- <https://www.thebci.org/static/e02a3e5f-82e5-4ff1-b8bc61de9657e9c8/BCI-0007h-Supply-Chain-Resilience-ReportLow-Singles.pdf>
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- <https://www.ey.com/en_gl/supply-chain/supply-chain-sustainability-2022>
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- <https://www.nstauthority.co.uk/media/8192/sc-report_final_accessible.pdf>
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- <https://www.bmz.de/de/themen/lieferkettengesetz>
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- <https://www.bgbl.de/xaver/bgbl/start.xav>#**bgbl**%2F%2F\*%5B%40attr_id%3D%27bgbl121s2959.pdf%27%5D\_\_1671334142633
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- <https://www2.deloitte.com/content/dam/Deloitte/de/Documents/risk/Deloitte_CSR_Brochure_final.pdf>
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## Components
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### Raspberry Pi
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| Criteria | Description |
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| --------------------- | ----------- |
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| Article | |
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| Manufacturer | |
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| Production country | |
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| Production conditions | |
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| Local availability | |
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| Transportation | |
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| Raw materials | |
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| Recycling | |
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| Waste | |
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| Risk | |
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| Alternatives | |
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| Implications | |
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### Source
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- business@raspberrypi.com
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- <http://www.designlife-cycle.com/raspberry-pi>
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### Notes
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### Camera Module
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- <http://www.designlife-cycle.com/image-sensor>
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Plankton imaging with the PlanktoScope: A
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setup and sampling guide
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Forked from Planktoscope protocol for plankton imaging
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Lombard Fabien, Will Major
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1 Works for me
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Will Major
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ABSTRACT
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This is a instructional manual for setting up the PlanktoScope (V2.5) for regular data
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collection and processing, as well as a step-by-step guide for running samples.
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ATTACHMENTS
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Pollina et al 2020
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2020.04.23.056978v1.full.
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pdf
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EXTERNAL LINK
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<https://www.planktoscope.org/>
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PROTOCOL INFO
|
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Lombard Fabien, Will Major . Plankton imaging with the PlanktoScope: A setup and
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sampling guide. protocols.io
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<https://protocols.io/view/plankton-imaging-with-the-planktoscope-a-setup-andb5znq75e>
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MANUSCRIPT CITATION please remember to cite the following publication along with this protocol
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Pollina T, Larson A, Lombard F, Li H, Colin S, Vargas C de, Prakash M (2020)
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PlanktonScope: Affordable modular imaging platform for citizen oceanography.
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bioRxiv 2020.04.23.056978. doi: 10.1101/2020.04.23.056978
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FORK FROM
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Forked from Planktoscope protocol for plankton imaging, Lombard Fabien
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KEYWORDS
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plankton, PlanktoScope, imaging, microscope
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IMAGE ATTRIBUTION
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Fabien Lombard, Thibaut Pollina, Will Major
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CREATED
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Mar 07, 2022
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LAST MODIFIED
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Jul 14, 2022
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1
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PROTOCOL INTEGER ID
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59150
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GUIDELINES
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PlanktoScope is an optical instrument. Its optical elements (camera, lenses, flowcell) are
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highly sensitive to dust and dirt. We recommend that you never touch any of those
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component with fingers and store the PlanktoScope in a dust free and humidity free area
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(or in a box when not used).
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MATERIALS TEXT
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PlanktoScope
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Plankton Net
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200 µm sieve
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Optical paper
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Pine Pollen in Water and Pine Pollen dry
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SAFETY WARNINGS
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Planktoscope is an electronic device, powered with electricity. It is therefore sensitive to
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water.
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- Place it in an environment where water can not enter in contact with the instrument and
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secure its electrical part.
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- Be careful when manipulating samples, take care of having the exhaust tube in a "trash"
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contained to avoid spillage.
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- Glass parts are present (flowcell) and should be handled with caution (to avoid injury)
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and kept clean (avoid touching it with fingers).
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BEFORE STARTING
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Make sure to read through an entire subsection before taking any action.
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Initial connection and setup
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1
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Powering, connecting to and configuring the PlanktoScope.
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This section will introduce you to using your PlanktoScope:
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- subsections 1.1 and 1.2 cover turning on and connection to the machine;
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- subsections 1.3 - 1.7 will cover running the necessary tests to make sure your PlanktoScope is
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working as we
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expect.
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Please ensure you carefully read through each subsection before you take any action.
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1.1
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Power your Planktoscope by connecting power cable to the power input and
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turning on the wall switch. Within 1 minute of turning on your PlanktoScope, you
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should see the LED flash once.
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After a few minutes, you should see a new option for Wi-fi appearing on your
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2
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|
||||
computer. Connect to it using the password: "copepode".
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For more information and alternative methods of connection, see the designer's
|
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Connectivity Tutorial here:
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|
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1.2
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|
||||
PlanktoScope - Connectivity Tutorial.pdf
|
||||
|
||||
Open the PlanktoScope's User Interface (UI) on your web browser (Chrome,
|
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Firefox, Edge etc.) using the following webpage link (either click on the link or
|
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copy and paste into your browser):
|
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<http://192.168.4.1:1880/ui/>
|
||||
There are several tabs on the UI that can be used to adjust setting, run samples
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and take images. To navigate around the UI, all tabs are available from the Home
|
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tab, including the Shutdown button which we will use when we have finished
|
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using the PlanktoScope.
|
||||
We can also use the 'Hamburger Menu', situated in the top-left corner of the UI, to
|
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navigate between tabs.
|
||||
|
||||
The 'Home' tab of PlanktoScope's User Interface.
|
||||
|
||||
The 'Hamburger Menu' icon, situated in the top-left corner of the screen, can be used to
|
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navigate around the User Interface
|
||||
|
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1.3
|
||||
|
||||
Once the UI has loaded on your browser, navigate to the Optic Configuration tab
|
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and we will make sure the PlanktoScope is operating correctly .
|
||||
|
||||
To test the PlanktoScope, navigate to the Optic Configuration tab:
|
||||
|
||||
3
|
||||
|
||||
The Optic Configuration tab which can be used to adjust the camera settings. If only Preview is visible
|
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on your screen, the other options should be available below by scrolling down or by adjusting 'Zoom'
|
||||
on your browser (usually Ctrl + scroll UP or DOWN on Windows or command + scroll UP or DOWN on
|
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Mac).
|
||||
|
||||
a) Under Optic Characterisation, switch on the Light by clicking 'On'. You should
|
||||
see the Preview image turning from dark to light. The Preview image could be
|
||||
any colour so do not worry if yours does not show blue; it will be adjusted later.
|
||||
|
||||
The red box highlights the location for turning on the LED. You will need to do this every time you use
|
||||
your PlanktoScope.
|
||||
|
||||
b) Under Focus Adjustment, click 'UP 1MM' and 'DOWN 1MM' to ensure focus
|
||||
buttons turn the focus motor. You should see the mount moving further from (UP)
|
||||
or closer to (DOWN) the camera.
|
||||
|
||||
4
|
||||
|
||||
Red boxes highlight 'UP 1MM' and 'DOWN 1MM' that will move the Mount (pictured below).
|
||||
|
||||
Green arrows highlight the movement of the Mount when using Focus Adjustment buttons on the Optic
|
||||
Configuration tab. 'UP 1MM' will move the Mount towards the right-hand side of the picture, while
|
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'DOWN 1MM' will move the Mount to the left-hand side of the picture.
|
||||
|
||||
c) Under Fluidic Manual Manipulation, click clockwise arrow to check that the
|
||||
Peristaltic Pump is working. You should see the pump rotating in an clockwise
|
||||
direction.
|
||||
|
||||
5
|
||||
|
||||
The red square highlights the location of the clockwise arrow that will rotate your Peristaltic Pump in
|
||||
the same direction.
|
||||
|
||||
The clockwise arrow from the Fluidic Manual Manipulation section should rotate your PlanktoScope's
|
||||
Peristaltic Pump in a clockwise direction.
|
||||
|
||||
d) Under Camera Settings, change the ISO value. You should see changes to the
|
||||
Preview image. After this test, Set ISO to 100 .
|
||||
6
|
||||
|
||||
The red box highlights the location of the ISO setting. You should see your Preview image change
|
||||
colour when you adjust this setting. Make sure it is set to 100 once you have tested this.
|
||||
|
||||
1.4
|
||||
|
||||
Now we will align the lenses in your PlanktoScope . To do this:
|
||||
a) Remove the Fluidic Path from the mount and gently lay to the side.
|
||||
|
||||
Remove the Fluidic Path and lay to the side
|
||||
|
||||
7
|
||||
|
||||
Remove the Fluidic Path and lay to the side
|
||||
|
||||
b) Make sure we have enough space to remove the lenses by clicking the 'UP
|
||||
1MM' button under Focus Adjustment.
|
||||
|
||||
Red box highlights 'UP 1MM' button that will move the Mount away from the lenses.
|
||||
|
||||
8
|
||||
|
||||
Move the Mount away from the lenses using the 'UP 1MM' button to allow for outer lens removal.
|
||||
|
||||
c) Remove the outermost lens (16MM).
|
||||
|
||||
9
|
||||
|
||||
Remove the outermost (16MM) lens.
|
||||
|
||||
d) On the Preview image on the Optic Configuration tab, you should see a light
|
||||
spot surrounded by darkness. By moving the 25MM lens on your PlanktoScope,
|
||||
you can move the light spot on the Preview image. Try to get the light spot as
|
||||
close to the centre of the Preview image as possible.
|
||||
|
||||
With the 16MM lens removed, your Preview image should resemble this picture. If the light spot is not
|
||||
centred, gently reposition the 25MM lens until it is as close to centre as you can get it.
|
||||
|
||||
10
|
||||
|
||||
Gently reposition the inner (25MM) lens.
|
||||
|
||||
e) Once centred, place the outermost lens back to where you removed it from
|
||||
in step 3.
|
||||
|
||||
Place the outer (16MM) lens back into position.
|
||||
|
||||
11
|
||||
|
||||
f) On the Preview, you may see darker areas in the corners. To get rid of the
|
||||
darker areas in the corner, reposition the outermost lens (16MM) while holding
|
||||
the innermost lens (25MM) steady; the darker corners should disappear. Try to
|
||||
achieve homogenous light across the Preview image.
|
||||
g) Place the Fluidic Path back into position.
|
||||
|
||||
1.5
|
||||
|
||||
Manually adjust the white balance of your PlanktoScope . Try pressing the
|
||||
Auto White Balance button to its 'on' and 'off' positions on the Optic Configuration
|
||||
tab; you will likely see the Preview image changing colour.
|
||||
We need to achieve the Preview image colour that the Auto White Balance
|
||||
feature provides, without using the Auto White Balance. Not using Auto White
|
||||
Balance enhances the performance of the PlanktoScope over time.
|
||||
To manually set to the White Balance, turn off the Auto White Balance and adjust
|
||||
WB: Red and WB: Blue until it looks white. Then switch AWB back on to see if it
|
||||
matches. Repeat this process until there is no colour change when clicking the
|
||||
AWB button.
|
||||
Set the AWB button to 'off' once you have completed this step.
|
||||
|
||||
12
|
||||
|
||||
The red box highlights how to manually adjust the white balance of the Preview image. In this example,
|
||||
the correct setting was WB: Red = 4 and WB: Blue = 1.21. The AWB button should be set to 'off' once
|
||||
you have completed this step.
|
||||
|
||||
1.6
|
||||
|
||||
Setup the 'Bubbler' :
|
||||
|
||||
Locate the Bubbler.
|
||||
|
||||
13
|
||||
|
||||
Tie a knot in the Bubbler.
|
||||
|
||||
Plug the Bubbler into one of the USB ports on the PlanktoScope.
|
||||
|
||||
14
|
||||
|
||||
Place the tubing into the Syringe so that it reaches the bottom.
|
||||
|
||||
Affix the tubing to the Syringe using an elastic band, string or similar.
|
||||
|
||||
15
|
||||
|
||||
1.7
|
||||
|
||||
Load in a practice sample and manually adjust the focus of the camera .
|
||||
a) Locate the Pine Pollen in Water sample and a Pasteur Pipette.
|
||||
|
||||
b) Shake the Pine Pollen in Water sample, remove the lid, and use the Pasteur
|
||||
Pipette to transfer roughly 10 mL into the Syringe. Take this opportunity to check
|
||||
that your Bubbler is working appropriately: you should see no more than 4-5
|
||||
bubbles per second. Tighten the knot in the tubing to reduce the airflow if you
|
||||
need to.
|
||||
|
||||
16
|
||||
|
||||
c) From the Optic Configuration tab, run the Peristaltic Pump so that the Flow
|
||||
System is filled with the sample. Double-check that the tubing from your
|
||||
Peristaltic Pump runs into the Waste (Test Tube with dark blue lid).
|
||||
|
||||
d) On the Optic Configuration tab under Focus Adjustment, use the 'UP 1MM'
|
||||
and 'DOWN 1MM' to adjust course focus , and 'UP 100UM' and 'DOWN 100UM' to
|
||||
17
|
||||
|
||||
adjust fine focus . You will likely need to use the 'DOWN 1MM' to move the
|
||||
Mount close to the lenses before using the fine focus buttons. You should see
|
||||
small dark particles on the Preview image; these particles need to be in perfect
|
||||
focus, adjust until correct.
|
||||
|
||||
Pine pollen particles in perfect focus in the Preview image.
|
||||
|
||||
You may see the edge of the flow system in your Preview image (see the red box). To fix this, simply
|
||||
reposition the outer lens (16MM) as we did in step 1 .5 f .
|
||||
|
||||
NB: if you do not see any particles, try adding a very small amount more of Pine
|
||||
Pollen to your Syringe by dipping the handle of a teaspoon into your dry Pine
|
||||
Pollen sample, and then into your Syringe sample. Then run the Peristaltic Pump
|
||||
once more to pass the sample with a higher concentration of Pine Pollen in front
|
||||
of the camera. Wash the spoon thoroughly after use.
|
||||
|
||||
18
|
||||
|
||||
The handle of a teaspoon dipped into dry Pine Pollen sample. Less is mo re!
|
||||
|
||||
1.8
|
||||
|
||||
To finish the setup , run the Pump from the Optic Configuration tab until all of
|
||||
the Pine Pollen sample has passed into the Waste. Fill the Syringe with tap water
|
||||
and run it through into the Waste to clean the PlanktoScope (you may need to
|
||||
empty the Waste into the sink/toilet before you do this).
|
||||
Shut down the PlanktoScope by navigating to 'Home', click the 'Unlock Button'
|
||||
and then click 'Shutdown'. Leave for one minute before turning off your
|
||||
PlanktoScope at the wall plug.
|
||||
|
||||
Get your sample
|
||||
|
||||
2
|
||||
|
||||
Using a net to collect a sample
|
||||
|
||||
2.1
|
||||
|
||||
Remove the net from its bag and set aside the 200 µm sieve.
|
||||
19
|
||||
|
||||
Within the net bag you will find the net (left of photo) and 200 µm sieve (right of photo).
|
||||
|
||||
- Position yourself close to but a safe distance from the water's edge and ensure
|
||||
a stable footing.
|
||||
- Unspool the rope.
|
||||
- Hold the lead weight on the rim of the net along with the cod end in your
|
||||
throwing hand while holding the plastic handle tightly with your other hand, throw
|
||||
the net into the water.
|
||||
- Gently pull the net back towards you just before it hits the water to orientate it.
|
||||
Pull the net back towards to at a speed so that it is submerged but does not sink.
|
||||
For areas of fast flow, you may only have to perform one cast. With areas of
|
||||
sluggish or no flow, two or three casts may be necessary.
|
||||
|
||||
2.2
|
||||
|
||||
To get the sample from the net:
|
||||
|
||||
- remove the cod end and spray its mesh sides with water from the Pasteur
|
||||
Pipette.
|
||||
|
||||
20
|
||||
|
||||
Remove the cod end from the net by twisting in an anti-clockwise direction. Ensure to keep the cod
|
||||
end upright.
|
||||
|
||||
Spray mesh sides of the cod end with water from the Pasteur Pipette to ensure all particles move
|
||||
down into your sample.
|
||||
|
||||
- Once you are satisfied that any particles are no longer stuck to the mesh sides,
|
||||
21
|
||||
|
||||
you are ready to transfer your sample into a Falcon Tube. While holding the
|
||||
200µm sieve above a Falcon tube, slowly pour your sample so that it passes
|
||||
through the sieve and into the tube. Label your Sample and keep a record of its
|
||||
date, time and location.
|
||||
|
||||
Position the 200 µm sieve above the Falcon Tube
|
||||
|
||||
Pour your sample from the cod end, through the sieve and into your Falcon Tube.
|
||||
|
||||
- Make sure you label your sample and keep a log of when and where you have
|
||||
collected it.
|
||||
22
|
||||
|
||||
- Ensure to rinse your net and sieve in fresh water before the next use.
|
||||
Running a sample
|
||||
|
||||
3
|
||||
|
||||
This section covers your regular use of the PlanktoScope, and the setup and procedure you will
|
||||
undertake each time you want to run a sample.
|
||||
|
||||
3.1
|
||||
|
||||
Navigate to the Sample tab to set up running a sample through the
|
||||
PlanktoScope.
|
||||
|
||||
The Sample tab on the PlanktoScope's UI
|
||||
|
||||
a) Begin inputting Sample Identification information.
|
||||
|
||||
Fill the entries shown by the red box:
|
||||
Project name = MAPPS
|
||||
Name of the operator = Your Name
|
||||
Station ID = Your sample location e.g River Thames or Southampton Water.
|
||||
|
||||
b) Input the 'Net Throw Location' information including Latitude, Longitude,
|
||||
Date and Time before clicking the 'VALIDATE' button. The format for this section
|
||||
is strict and can be a bit of a fiddle; if you have not input the information perfectly
|
||||
23
|
||||
|
||||
when you click 'VALIDATE', you will have to input the information from scratch.
|
||||
The next few images will show you how to input these pieces of information.
|
||||
|
||||
b) i. Latitude and Longitude
|
||||
Use your web browser and navigate to <https://www.google.com/maps>
|
||||
|
||||
ii. Click on your sample collection location on Google Maps and you should see a grey symbol that
|
||||
matches that in the red circle. If you do not see this symbol, try to adjust the position of your click
|
||||
slightly.
|
||||
iii. You will see coordinates in the red square (above), click on these numbers.
|
||||
|
||||
24
|
||||
|
||||
iv. The relevant information is the numbers in the red box (above) that are separated by a comma.
|
||||
Copy (Ctrl + C for Windows or command + C for Mac) the first number and paste (Ctrl + V for
|
||||
Windows or command + V for Mac) it into the Latitude entry on the Sample tab.
|
||||
The second number may have a minus sign before it. Do not include this. Copy the second number
|
||||
(without the minus sign) and paste it into the Longitude entry on the Sample tab.
|
||||
You then need to include °N in the Latitude box, and °E or °W depending on whether there was a minus
|
||||
sign before the number (minus = °W; no minus = °E). The easiest way to enter the degree symbol will
|
||||
be to copy and paste it from this document. Alternatively, on Windows you can press Alt + 0176 and
|
||||
on Mac you can press Shift + Option + 8.
|
||||
|
||||
v. Then enter the Date (and time) of your data collection (as in, the date and time
|
||||
you had your net in the water) in the format listed e.g. 2022-03-11 12:00
|
||||
vi. Then enter Time e.g. 12:00. Please ensure that the time in the Date section
|
||||
and Time sections match.
|
||||
vii. Click 'VALIDATE'
|
||||
|
||||
3.2
|
||||
|
||||
Run a sample by navigating to the Fluidic Acquisition tab.
|
||||
In the red box pictured below, update the following parameters:
|
||||
a) Acquisition Unique ID should be a three-digit number starting with 001 and
|
||||
25
|
||||
|
||||
increasing with each sample you run.
|
||||
b) Number of images to acquire should be 100
|
||||
c) Pumped Volume (mL) should be around 0.1
|
||||
d) Delay to stabilise image should be 0.5
|
||||
e) Flowcell should be 300 μm Capillary.
|
||||
|
||||
Once you have updated the parameters correctly, click 'UPDATE CONFIG'. Then,
|
||||
click 'START ACQUISITION' and the Pump and imager should start.
|
||||
|
||||
3.3
|
||||
|
||||
Once you have run your sample and collected the images, you will need to
|
||||
segment them (separate each image into images of individual particles).
|
||||
Navigate to the Segmentation tab.
|
||||
|
||||
1. Click on the "update acquisition's folder list"
|
||||
2. Select the samples you wish to segment
|
||||
3. Setup the different options of the segmenter (see below for idealised setup).
|
||||
26
|
||||
|
||||
- Recursive folder means that it will segment all samples within a selected
|
||||
sample
|
||||
|
||||
- Ecotaxa archive: it will create a zip file containing all files needed for a easy
|
||||
importation within ecotaxa
|
||||
- Force rework: if yes it will re-segment samples already segmented
|
||||
- Keep objects: it will keep the final segmented images visible in the planktoscope
|
||||
(that could be accessed by the gallery in the objects folder)
|
||||
|
||||
The idealised Control setup for segmenting images within the PlanktoScope User Interface
|
||||
|
||||
4. Scroll down and clic on start segmentation
|
||||
5. Wait for the segmenter status to turn to "Done"
|
||||
|
||||
6. Finally, download your segmented images from the PlanktoScope using
|
||||
FileZilla (described in section 4)
|
||||
Download your Plankton images
|
||||
|
||||
4
|
||||
You will need a computer connected to the planktoscope together with free software FileZilla
|
||||
(<https://filezilla-project.org/>)
|
||||
Open FileZilla
|
||||
Either click on the top right to create a new connection or use the quick-connection fields
|
||||
below
|
||||
Enter the following informations:
|
||||
Host: s<ftp://planktoscope.local> (192.168.4.1 should also works)
|
||||
27
|
||||
|
||||
Username: pi
|
||||
Password: copepode
|
||||
Port: 22
|
||||
|
||||
click on connect
|
||||
on the bottom panels you have (on the left) the access to what is in your computer and (on the
|
||||
right) the access to what is in the planktoscope (click and slide to transfer data in between
|
||||
both)
|
||||
|
||||
Exports file for EcoTaxa are in /home/pi/data/export/ecotaxa
|
||||
Raw images files are in /home/pi/data/img
|
||||
Different control files to check the segmentation process (../images after background substraction,
|
||||
masks of the different objects etc) are in /home/pi/data/clean
|
||||
Final vignettes are in /home/pi/data/objects
|
||||
Once you have downloaded the images, you can clean and shutdown your PlanktoScope (see the
|
||||
next section), and reconnect to the internet.
|
||||
Clean the planktoscope
|
||||
|
||||
5
|
||||
|
||||
1. Drain the sample out of the syringe
|
||||
2. Disconnect the syringe and clean it with tap water (or even distilled water)
|
||||
3. Pump (at high speed!) the full content of the fluidic system to remove any liquid
|
||||
4. Reconnect the syringe
|
||||
5. Fill it with tap water (or distilled water)
|
||||
6. Pump (at high speed!) while regularly pinch the tubing to detach any plankton in the system
|
||||
(see
|
||||
|
||||
)
|
||||
|
||||
7. Drain again the syringe (repeat steps 7.2-7.7 at least 2 more times until no plankton is
|
||||
visible on the camera)
|
||||
8. Finally drain the system
|
||||
Shut down the PlanktoScope by navigating to 'Home', click the 'Unlock Button' and then clicking
|
||||
'Shutdown'. Leave for one minute before turning off your PlanktoScope at the wall plug.
|
||||
28
|
||||
|
||||
Upload your images on EcoTaxa
|
||||
|
||||
6
|
||||
At First connection:
|
||||
Create an account on EcoTaxa (<https://ecotaxa.obs-vlfr.fr/>) by clicking on the top right "log
|
||||
in/register"
|
||||
|
||||
Put your real name and a valid mail so that you can be contacted
|
||||
|
||||
29
|
||||
|
||||
6.1
|
||||
|
||||
Once logged you can consult the project on which you are registered by clicking
|
||||
onto "contribute to a project " on the main page.
|
||||
Our project is called #4970 PlanktoScope - MAPPS - 2021
|
||||
You must first notify a project manager who will assign you permissions
|
||||
|
||||
6.2
|
||||
|
||||
upload the ecotaxa archives (see step 4) on the EcoTaxa ftp
|
||||
using Filezilla (see
|
||||
|
||||
) create a connection by using the following information:
|
||||
|
||||
Select File > Site Manager...
|
||||
Create a New Site called : Ecotaxa_VLFR
|
||||
In General tag :
|
||||
Host : plankton.obs-vlfr.fr
|
||||
Protocol : FTP – File Transfer Protocol
|
||||
Encryption : Only use plain FTP (insecure)
|
||||
Logon Type : Normal
|
||||
User : ftp_plankton
|
||||
Password : Pl@nkt0n4Ecotaxa
|
||||
30
|
||||
|
||||
Once this is done you could use FileZilla to load the Zip files downloaded from the
|
||||
Planktoscope onto the EcoTaxa ftp server (e.g.
|
||||
/Ecotaxa_Data_to_import/PLANKTONSCOPE)
|
||||
|
||||
Please eventually create your own folder to "try" to keep it clean and
|
||||
tidy
|
||||
Please think to regularly remove those temporary files from the ftp,
|
||||
at this point they are not secured at all and everybody can access
|
||||
them (and disk space is not free)
|
||||
|
||||
6.3
|
||||
|
||||
In the project on your 'Project' options button, select import images and metadata
|
||||
|
||||
6.4
|
||||
|
||||
locate your file on the ecotaxa ftp folders and import it (only works for one zip file
|
||||
at a time for now)
|
||||
|
||||
31
|
||||
|
||||
Maintenance of your planktoscope
|
||||
|
||||
7
|
||||
|
||||
Clean tubing and flowcell from inside
|
||||
imaging plankton will lead to have a lot of organic material and seawater in the fluidic system.
|
||||
Some may clog or accumulates in some parts of the fluidic system.
|
||||
|
||||
1. Don't let it dry and try to get rid of it as soon as possible (if its occurs during sample acquisition,
|
||||
even abort this latter, take care of the clog, maybe dilute the sample
|
||||
acquisition while noting that the sample got diluted in the metadata
|
||||
|
||||
and restart
|
||||
)
|
||||
|
||||
2. Pump tap or distilled water with high pumping rates helps to unclog the system. make sure no
|
||||
plankton organisms remain in the fluidic system and especially on the internal walls of the
|
||||
flowcell. If it is the case don't hesitate to pinch (during 1-2 second) and release the tubing
|
||||
between the flowcell and the pump while pumping to create a sudden variation of pressure
|
||||
(e.g.
|
||||
|
||||
)
|
||||
|
||||
3. Over time, wet conditions and organic matter may create favorable condition for the growth of
|
||||
a bacterial film. The flowcell and tubing will look dirty from the inside. You can avoid this by
|
||||
pumping diluted bleach sometimes, let it act for 1-2 hours and carefully rinse the whole
|
||||
system
|
||||
4. Water, bacteria, and bleach together may favour the apparition of a calcium carbonate film
|
||||
inside the tubing and flowcell. It may either appear as dispersed cristals attached inside the
|
||||
flowcell or a white coating inside the tubing. To remove and clean this, pump some acidic
|
||||
solution (vinegar, citrus juice or other kind of other acids), let it rest for a few hours and rinse
|
||||
the system
|
||||
Clean flowcell outside:
|
||||
The flowcell is an optical critical component, keeping it clean is an absolute necessity. Don't touch
|
||||
it with fingers or other kind of dirty material. If dirty:
|
||||
1. if only dry dusts are present, gently blow the flowcell (ideally with dry gas dispenser at a large
|
||||
distance - dry gas dispenser are also creating thermal chocs if used from too close, test it on
|
||||
other material before)
|
||||
2. if dirt in not only dry dusts it could be cleaned with optical paper and ethanol. DO NOT USE
|
||||
CLASSICAL WIPING PAPER which are usually enriched in silica fibers for solidity ... and
|
||||
may create scratches on the flowcell. (disposable nose tissue are better alternative if optical
|
||||
paper is not available)
|
||||
|
||||
Clean optical lenses
|
||||
as for the flowcell, optical lenses are critical elements of your planktoscope and should be kept as
|
||||
clean as possible. It starts by never touching them with fingers (cleaning those would requires a
|
||||
lot of patience, efforts and may even lead to unexpected disappointments)
|
||||
|
||||
1. dry dust: dry gas (with even more caution than previously
|
||||
2. others: only used optical paper
|
||||
clean the camera sensor
|
||||
... critical part if any, NEVER touch it, only use dry gas
|
||||
regularly calibrate the pump
|
||||
External links
|
||||
|
||||
8
|
||||
|
||||
Planktoscope website
|
||||
<https://www.planktoscope.org/>
|
||||
32
|
||||
|
||||
Planktoscope github
|
||||
<https://github.com/PlanktonPlanet/PlanktoScope>
|
||||
Planktoscope complete assembly guide and complete documentations
|
||||
<https://planktonscope.readthedocs.io/en/latest/>
|
||||
Planktoscope Slack channel (to exchange ideas/protocols/solutions)
|
||||
<https://forms.gle/qvh5jwuMvmyBKMQC7>
|
||||
Plankton Planet website
|
||||
<https://planktonplanet.org/>
|
||||
EcoTaxa tutorials:
|
||||
<https://sites.google.com/view/piqv/ecotaxa?authuser=0>
|
||||
<https://www.youtube.com/watch?v=PSO6ZS765tk>
|
||||
<https://www.youtube.com/watch?v=RaWUqIoKk0E>
|
||||
|
||||
33
|
||||
|
|
@ -11,11 +11,8 @@ nav:
|
|||
- Research: research.md
|
||||
- Hardware:
|
||||
- Manufacturing Guide: hardware/manufacturing.md
|
||||
# - Supply Chain: hardware/supply_chain.md
|
||||
- Assembly Guide: hardware/assembly_guide.md
|
||||
# - Assembly Guide old: hardware/assembly_guide_org.md
|
||||
- Maintenance and Repair Guide: hardware/maintenance_repair.md
|
||||
# - Disposal and recycling: hardware/disposal_recycling.md
|
||||
- Planktoscope HAT: hardware/hat_hardware.md
|
||||
- Accessories: hardware/accessories.md
|
||||
- Software:
|
||||
|
|
@ -28,8 +25,6 @@ nav:
|
|||
- User Interface: usage/ui_guide.md
|
||||
- Remote Access: usage/remote_access.md
|
||||
- MQTT Messages: usage/mqtt_messages.md
|
||||
# - Protocols:
|
||||
# - Basic Primer: protocols/basic_primer.md
|
||||
- Contribute:
|
||||
- Github Workflow: contribute/github_workflow.md
|
||||
- Hardware Development: contribute/hardware_development.md
|
||||
|
|
@ -40,7 +35,6 @@ nav:
|
|||
- User Groups: community/usergroups.md
|
||||
- Trainings: community/trainings.md
|
||||
- Code of Conduct: community/code_of_conduct.md
|
||||
# - Funding: funding.md
|
||||
- FAQ: faq.md
|
||||
- License: license.md
|
||||
- Changelog: changelog.md
|
||||
|
|
|
|||
Loading…
Reference in New Issue