converting phytoplankton images into vector graphics and creating phytoplankton patterns

Exploring Long-Term Shifts in Phytoplankton by Conversion of Microscopic Images

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.

저자 스포트라이트: 시계열 데이터와 예술적 표현을 통한 기후 변화에 대한 플랑크톤의 대응 발표 

식물성 플랑크톤의 장기적인 변화를 묘사하기 위한 해양학적 데이터 시각화

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  

식물성 플랑크톤 이미지를 벡터 그래픽으로 변환하고 식물성 플랑크톤 패턴 만들기

시작하려면 Narragansett Bay Long-Term Plankton Time Series에서 촬영한 식물성 플랑크톤 현미경 이미지를 JPEG, PNG 또는 PDF 파일로 선택합니다. JPEG 또는 PNG 현미경 이미지를 Illustrator 작업 영역에 가져옵니다. View(보기)로 이동한 다음 Show Transparency Grid(투명 격자 표시)를 클릭하여 투명 영역을 나타내는 바둑판 배경을 표시합니다.그런 다음 창(Window)을 클릭한 다음 드롭다운 메뉴에서 이미지 추적(Image Trace) 을 클릭하여 이미지 추적 창을 엽니다. 이미지 추적 옵션에서 Preset(사전 설정), Black and White Logo(흑백 로고), Mode(모드), Black and White(흑백)를 차례로 클릭합니다. 그런 다음 Properties(속성)에서 Expand(확장)를 선택하여 벡터화합니다.직접 선택 도구를 선택하고 공백을 클릭합니다. 삭제한 다음 파일 및 다른 이름으로 저장을 클릭하고 EPS 벡터 그래픽으로 저장을 선택합니다. 식물성 플랑크톤 패턴을 만들려면 먼저 도구 모음에서 사각형 대지 도구를 클릭하여 새 작업 영역에 새 대지를 만듭니다.속성 내에서 크기를 조정하여 동일한 크기의 동일한 아트보드 3개를 만듭니다. 다양한 식물성 플랑크톤 분류군의 EPS 파일을 아트보드로 드래그 앤 드롭합니다. 직접 선택 도구를 사용하여 개별 식물성 플랑크톤 주위에 상자를 그립니다.Properties(속성)에서 Embed(포함)를 선택한 다음 Fill(채우기)을 선택하고 10년을 대표하는 색상표에서 원하는 색상으로 식물성 플랑크톤을 채색합니다. 그런 다음 검은색 화살표 선택 도구를 사용하여 특정 식물성 플랑크톤을 강조 표시합니다. Edit(편집), Copy(복사), Edit(편집)를 차례로 선택하고 Paste(붙여넣기)를 클릭합니다.각 식물성 플랑크톤 벡터를 30년 동안 데이터 세트에 있는 각 분류군의 상대적 비율을 기반으로 정성적으로 붙여넣습니다. Object, Pattern, Make를 차례로 선택하여 30년 각각에 대한 색상 견본 식물성 플랑크톤 패턴을 만듭니다.

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Converting Phytoplankton Images into Vector Graphics and Creating Phytoplankton Patterns

100 조회수.  University of Rhode Island. 시작하려면 Narragansett Bay Long-Term Plankton Time Series에서 촬영한 식물성 플랑크톤 현미경 이미지를 JPEG, PNG 또는 PDF 파일로 선택합니다. JPEG 또는 PNG 현미경 이미지를 Illustrator 작업 영역에 가져옵니다. View(보기)로 이동한 다음 Show Transparency Grid(투명 격자 표시)를 클릭하여 투명 영역을 나타내는 바둑판 배경을 표시합니다.그런 다음 창(Window)을 클릭한 다음 드롭다운 메뉴에서...

비디오: 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 ...

연구

환경과학

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.