Sample collection
Collecting samples from lakes and ocean and preparing them for microscopy
Microscopy
Employing the open source platform OpenFlexure Microscope for automated photography
Image analysis
Using open source libraries to develop Ai-assisted identification and quantification methods
Environmental monitoring and the need of more data
Our ability to understand the environment depends on our capacity to collect and analyse data. Access to cost effective means to collect data makes it possible to more clearly visualise temporal and spatial distribution of aquatic microorganisms, at a time when a rapidly changing climate pose an increasingly significant stress factor on aquatic ecosystems.Recent years advances in, and availability of, open-source hardware (through 3D printer technology) and open-source software (AI and machine learning) has enabled for a paradigm shift when it comes to manufacturing and implementation of cost-effective scientific equipment (open-source platforms). This facilities for the collection of more data as well for the development of user-friendly instruments inviting more people participate and contribute to environmental research.
The BysjöBot Project aims to compile and share documentation guiding through the steps of manufacture and establishment of open-source platforms for the purpose of generating and analysing aquatic microscopic image data. This workflow cover the steps going from Sample collection through processesing (Microscopy and Image analysis) to Data visualisation.
Why do we need more data?
Microscopic organisms play a vital role in the global ecosystem. With their geochemical importance, being involved in fixation and regeneration of organic building blocks (carbon, nitrogen, sulphur and phosphorous) as well as producing the majority of atmospheric oxygen, they are the fundament in the aquatic food web and the backbone in our global ecosystem. At the same time, algae blooms can have devastating effects on local ecosystems causing toxic build-up and decimating the opportunities for other lifeforms. For us, access to healthy lakes and oceans is a prerequisite for drinking water production, recreation (e. g outdoor life and swimming) and business activities (e. g aquaculture and fishing).The rapidly changing climate is undoubtably contributing to rapid changes in the geographic distribution of microscopic organisms (biogeography). Many freshwater and marine ecosystems are placed at high risks of biodiversity loss according to the Intergovernmental Panel on Climate Change's assessment report of 2022.
It is difficult to argue that there is enough data to fully grasp the effects of climate change. Sweden's national databases for environmental data has in recent decades only seen a marginal growth in the amount of annual incoming data. One of the reasons is that there has not been any major technical methodological invention, and the collection of environmental data, especially from aquatic environments, is hampered by costly and time-consuming methodology.
In times of rapidly changing climate the ability to regularly measure spatial and temporal distribution of aquatic microorganisms is key when trying to understand the dynamics of climate change and its effects on aquatic ecosystems.
This project aims to further equip our society with tools to be able to detect harmful ecologically degrading developments and thus buying us more time to react and enforce countermeasures.
Links and descriptions to related solutions and protocols will be made available in the near future.
This webbpage, with all its contents, is to be considered under contruction and not a final product.