converting phytoplankton images into vector graphics and creating phytoplankton patterns

Esplorazione dei cambiamenti a lungo termine nel fitoplancton mediante conversione di immagini microscopiche

Phytoplankton are primary producers representing the base of the food web across aquatic ecosystems1,2. While phytoplankton monitoring programs are key to identifying current and future changes in marine ecosystems, their support is declining over time 3. Due to their relatively short generation times and limited mobility, phytoplankton are particularly responsive to climate change, which makes them an important tool in time series monitoring. Phytoplankton time series are also important for informing ecosystem-based management of resource availability&#160;and providing context for episodic events, such as marine heatwaves4. Short-term time series, on the matter of years, give insights into phytoplankton community succession and seasonal dynamics (e.g., ref.5,6), whereas long-term time series, such as the Bermuda Atlantic Time Series (BATS) and Hawaii Ocean Times Series (HOTS) Programs, span&#160;more than two decades and enable the detection of long-term trends7,8. Such studies illustrate the benefit and importance of a highly resolved phytoplankton record for a complete understanding of long-term ecosystem change in dynamic marine environments. Further, visualizing and communicating these changes in phytoplankton, which cannot be seen by the naked eye, are more difficult to comprehend than for organisms that are large and readily visible, like fish and whales. Computer visualizations offer a technique to explore complex data sets9 and improved illustrative graphics are becoming readily available (e.g., Integration and Application Network, University of Maryland Center for Environmental Science). However, most studies in phytoplankton ecology, including many referenced here, still only present results as data graphs reducing their accessibility to general audiences. Given that phytoplankton represent the base of the food web in most marine systems, communicating their importance to the nearly 2.4 billion people who live within the coastal ocean is critical10. Here, we developed a protocol with the goal of visualizing the diversity and magnitude of phytoplankton, as collected by a phytoplankton monitoring program.
The Narragansett Bay Plankton Time Series (NBPTS) provides a long-term 60+ year (1959-Present) perspective on the effects of global change within a climate context on phytoplankton abundance, seasonality, and phenology (life history). Narragansett Bay (NBay) is a coastal estuary connected to the broader systems of the U.S. Northeast Shelf and Northwest Atlantic whose production has important implications for fisheries and human use along the coastal U.S.A.11. NBay is considered a highly seasonal system experiencing long-term (1950-2015) warming waters in the region as well as shifts in nutrients and an increase in water clarity12,13. In addition, a decline in phytoplankton biomass has occurred in upper NBay related to anthropogenic decreases in dissolved inorganic nitrogen, which is partially attributed to upgrades in wastewater treatment plants12. Shifts in phytoplankton taxa, particularly harmful algal blooms (HABs), are also occurring in NBay. Pseudo-nitzschia spp., which produces pervasive toxic blooms in upwelling regions along the U.S. west coast, led to notable shellfish closures for the first time in NBay&#39;s history&#160;in 2016 and 201714,15,16. Communicating these changes to diverse audiences is important for increasing science literacy and for promoting continued support of phytoplankton monitoring studies.
The goal of this project was to utilize microscopic images of phytoplankton from NBay, as well as data synthesized from NBPTS, to visualize the literal shifts in phytoplankton taxa and biomass that are occurring in NBay to communicate and enhance the importance of phytoplankton to general audiences. NBPTS provides 60+ years of publicly available weekly phytoplankton counts and biomass to leverage data from (https://web.uri.edu/gso/research/plankton/). The final product was a large mural of plankton patterns representative of the time series data (e.g., phytoplankton biomass and taxa, temperature) within the art piece itself. This approach represents a visualization method that can be utilized for many other plankton time series throughout the world and can be adapted for monitoring programs with short-term, seasonal data as well. The benefits of implementing this protocol include increasing efforts in data visualization, science communication, education, and engagement with local communities.

Autore in primo piano: Svelare la risposta del plancton al cambiamento climatico attraverso i dati delle serie temporali e l'espressione artistica 

Visualizzazione di dati oceanografici per rappresentare i cambiamenti a lungo termine nel fitoplancton

I am a plankton ecologist focused on characterizing the effects of rapid climate change on phytoplankton and zooplankton ecology and physiology. Plankton ecology requires both a mix of traditional and modern approaches. More recently, plankton imaging technology, in addition to microscopy, is being used to quantify and measure plankton.This technology decreases the time it takes to manually count plankton by utilizing artificial intelligence to count and classify plankton for us. This research visualizes one of the longest plankton time series in the world. These data sets are critical for providing context to understanding shifts in plankton communities and food webs in regions affected by rapid climate change.My research has helped to visualize the mechanisms underpinning those shifts. Given the microscopic nature of plankton, it can be difficult, particularly for scientists to visualize in communicate how plankton communities are changing over time. My protocol aims to provide a clear method for visualizing shifts in plankton communities, leveraging scientific data within an artistic framework.This protocol will hopefully encourage the other scientists to think more creatively about how they visualize and present their data, particularly to non-sized audience. There is open gap between lab result and how they are interpreted and present in society. So, I hope this protocol will help reach this gap.My lab will continue to leverage plankton time series data sets to identify the environmental factors affecting long-term changes in plankton communities, as well as conduct physiological experiments in the lab to understand the physiologic mechanisms underpinning these community ships in the northeast United States and beyond.

Watch this Scientific Journal Video about Converting Phytoplankton Images into Vector Graphics and Creating Phytoplankton Patterns at JoVE.com

Converting Phytoplankton Images into Vector Graphics and Creating Phytoplankton Patterns  

Conversione di immagini di fitoplancton in grafica vettoriale e creazione di modelli di fitoplancton

Per iniziare, seleziona le immagini microscopiche del fitoplancton prese dalla serie temporale del plancton a lungo termine della baia di Narragansett come file JPEG, PNG o PDF. Inserite un'immagine microscopica JPEG o PNG nell'area di lavoro di Illustrator. Vai su Visualizza, quindi fai clic su Mostra griglia di trasparenza per visualizzare lo sfondo a scacchiera che indica le aree trasparenti.Quindi, fai clic su Finestra, seguito da Ricalco immagine nel menu a discesa per aprire la finestra Ricalco immagine. Sotto le opzioni Ricalco immagine, fare clic su Predefinito, quindi su Logo in bianco e nero, quindi su Modalità e Bianco e nero. Quindi, in Proprietà, seleziona Espandi per vettorializzarlo.Scegli lo strumento di selezione diretta e fai clic sullo spazio bianco. Eliminarlo, quindi fare clic su File e salva con nome e selezionare EPS da salvare come grafica vettoriale. Per creare modelli di fitoplancton, per prima cosa, crea una nuova tavola da disegno in una nuova area di lavoro facendo clic sullo strumento Tavola da disegno quadrata nella barra degli strumenti.Crea tre tavole da disegno identiche della stessa dimensione regolando le dimensioni all'interno di Proprietà. Trascina e rilascia i file EPS dei diversi taxa di fitoplancton sulla tavola da disegno. Usa lo strumento di selezione diretta per disegnare un riquadro attorno a un singolo fitoplancton.In Proprietà, selezionare Incorpora, quindi Riempi e colorare il fitoplancton con il colore desiderato dalla tavolozza dei colori, che è rappresentativo del decennio. Quindi usa lo strumento di selezione della freccia nera per evidenziare un particolare fitoplancton. Seleziona Modifica, quindi Copia, seguito da Modifica e fai clic su Incolla.Incolla qualitativamente ogni vettore di fitoplancton in base alle proporzioni relative di ciascun taxa nel set di dati per ciascuna delle tre decadi. Selezionare Oggetto, quindi Motivo e Crea per creare un modello di fitoplancton campione di colore per ciascuna delle tre decadi.

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Research

JoVE Journal

Environment

Converting Phytoplankton Images into Vector Graphics and Creating Phytoplankton Patterns

101 Views.  University of Rhode Island. Per iniziare, seleziona le immagini microscopiche del fitoplancton prese dalla serie temporale del plancton a lungo termine della baia di Narragansett come file JPEG, PNG o PDF. Inserite un'immagine microscopica JPEG o PNG nell'area di lavoro di Illustrator. Vai su Visualizza, quindi fai clic su Mostra griglia di trasparenza per visualizzare lo sfondo a scacchiera che indica le aree trasparenti.Quindi, fai clic su Finestra, seguito da Ricalco immagine nel menu a discesa per aprire la f...

Video: Converting Phytoplankton Images into Vector Graphics and Creating Phytoplankton Patterns  

Visualizing Oceanographic Data to Depict Long-term Changes in Phytoplankton

Oceanographic time series provide&#160;an important perspective on environmental processes in ecosystems. The Narragansett Bay Long-Term Plankton Time Series (NBPTS) in Narragansett Bay, Rhode Island, USA, represents one of the longest plankton time series (1959-present) of its kind in the world and presents a unique opportunity to visualize long-term change within an aquatic ecosystem. Phytoplankton represent&#160;the base of the food web in most marine systems, including Narragansett Bay. Therefore, communicating their importance to the 2.4 billion people who live within the coastal ocean is critical. We developed a protocol with the goal of visualizing the diversity and magnitude of phytoplankton by utilizing Adobe Illustrator to convert microscopic images of phytoplankton collected from the NBPTS into vector graphics that could be conformed into repetitive visual patterns through time. Numerically abundant taxa or those that posed economic and health threats, such as the harmful algal bloom taxa, Pseudo-nitzschia spp., were selected for image conversion. Patterns of various phytoplankton images were then created based on their relative abundance for select decades of data collected (1970s, 1990s, and 2010s). Decadal patterns of phytoplankton biomass informed the outline of each decade while a background color gradient from blue to red was used to reveal a long-term temperature increase observed in Narragansett Bay. Finally, large, 96-inch by 34-inch panels were printed with repeating phytoplankton patterns to illustrate potential changes in phytoplankton abundance over time. This project enables visualization of literal shifts in phytoplankton biomass, that are typically invisible to the naked eye while leveraging real-time series data (e.g., phytoplankton biomass and abundance) within the art piece itself. It represents an approach that can be utilized for many other plankton time series for data visualization, communication, education, and outreach efforts.

Here, we present a protocol for converting phytoplankton microscopic images into vector graphics and repetitive patterns to enable visualization of shifts in phytoplankton taxa and biomass over 60 years. This protocol represents an approach that can be utilized for other plankton time series and datasets globally.

Oceanographic time series provide&#160;an important perspective on environmental processes in ecosystems. The Narragansett Bay Long-Term Plankton Time ...

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To begin, select phytoplankton microscopic images taken from the Narragansett Bay Long-Term Plankton Time Series as either JPEG, PNG, or PDF files. Place JPEG or PNG microscopic image into the Illustrator workspace. Go to View, then click Show Transparency Grid to reveal the checkerboard background indicating transparent areas.Next, click on Window, followed by Image Trace in the dropdown menu to open the Image Trace window. Under the Image Trace options, click Preset, then Black and White Logo, followed by Mode and Black and White. Then under Properties, select Expand to vectorize it.Choose the direct selection tool and click on the white space. Delete it, and then click File and Save As, and select EPS To save as a vector graphic. To create phytoplankton patterns, first, create a new artboard in a new workspace by clicking the square Artboard tool in the toolbar.Make three identical artboards of the same size by adjusting the size within Properties. Drag and drop the EPS files of the different phytoplankton taxa onto the artboard. Use the direct selection tool to draw a box around an individual phytoplankton.Under Properties, select Embed, then Fill, and color the phytoplankton with the desired color from the color palette, which is representative of the decade. Then use the black arrow selection tool to highlight a particular phytoplankton. Select Edit, then Copy, followed by Edit, and click on Paste.Paste each phytoplankton vector qualitatively based on the relative proportions of each taxa in the dataset for each of the three decades. Select Object, then Pattern, and Make to create a color swatch phytoplankton pattern for each of the three decades.

Creating Phytoplankton Panels from Biomass and Temperature Data

Begin by opening a JPEG or PNG figure of the chlorophyll a decadal biomass into the Illustrator workspace. Then vectorize each of the three chlorophyll a seasonal cycles by removing the background and saving the image as an EPS file. Then create a new art board in a new Illustrator workspace by clicking and dragging the square art board tool in the toolbar.Adjust the size by clicking on properties and transform to make three identical art boards of the same size. Drag and drop the chlorophyll a EPS files onto the three art boards. Go to properties and embed to add it to the new art board.Create a new layer by selecting the sticky note icon. Next, create a rectangle within the new layer with the rectangle tool from the toolbar. Fill the rectangle with a light blue gradient using the gradient tool from the toolbar.Use the line segment tool from the toolbar to create a box attached to the trend line. Make the line straight and aligned by holding the Shift button, then press the Ctrl key and select all the components, including the lines and trend line, within the layer. Then select object, followed by path and join.Repeat creating a rectangle and fill it with a blue to red color gradient to represent warming water temperature across the three decadal panels. Create a third rectangle of equal size and fill it with the phytoplankton swatch pattern corresponding to that decade. Place the grouped line segments within the layer of rectangles.Next, select the two smaller rectangles and the grouped line segments. Select object, then clipping mask, followed by make. This will remove the top fill of the shape.Repeat creating a rectangle and fill it with a red to blue color gradient to represent a warming water temperature across the three decadal panels. To add images of microscopic phytoplankton onto the phytoplankton patterns, select open and click on the image file to open it in the Illustrator. Then create a circle with the ellipse tool from the toolbar and overlay it on top of the phytoplankton image.Hold the Shift key to select both the shape and the image. Then in the menu, click on object, then clipping mask, followed by make to fill the shape with the image. Repeat for selected phytoplankton images, and distribute across the three decades to look like a magnifying glass zooming in on the illustrative phytoplankton.Now use the rectangle tool from the toolbar to create a text box on each of the decade art boards. Use the type tool to click and type information about each decade. Add text at the top of each decade with the name of the decade, and add the names of the corresponding seasons at the bottom of each of the three panels.Import the saved Illustrator file and select to only import the three completed decades. Select all and export as a PDF file. Print the panels on heavyweight matter paper and install with hanging hardware.Visualization of phytoplankton data showed a decline in phytoplankton biomass from the 1970s to 1990s to 2010s. All decades exhibited a bimodal peak in chlorophyll a concentration with the first peak occurring in winter and the second occurring in summer. Also, Thalassiosira and Skeletonema species increased from the 1970s to 1990s.Other taxa, such as Eucampia, oscillated in abundance, as shown by the increased presence of more Eucampia zodiacus images in the 2010s compared to the 1970s and 1990s.