Name: Converting Phytoplankton Images into Vector Graphics and Creating Phytoplankton Patterns
Uploaded: 2023-07-28T13:40:00
Description: 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

חקר שינויים ארוכי טווח בפיטופלנקטון באמצעות המרה של תמונות מיקרוסקופיות

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.

מחבר זרקור: חשיפת תגובת פלנקטון לשינויי אקלים באמצעות נתוני סדרות זמן וביטוי אמנותי 

תצוגה חזותית של נתונים אוקיינוגרפיים כדי לתאר שינויים ארוכי טווח בפיטופלנקטון

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  

המרת תמונות פיטופלנקטון לגרפיקה וקטורית ויצירת תבניות פיטופלנקטון

כדי להתחיל, בחרו תמונות מיקרוסקופיות של פיטופלנקטון שנלקחו מסדרת זמן הפלנקטון לטווח ארוך של מפרץ נרגנסט כקובצי JPEG, PNG או PDF. מקמו תמונה מיקרוסקופית מסוג JPEG או PNG בסביבת העבודה של Illustrator. עברו אל 'תצוגה' ולאחר מכן לחצו על 'הצג רשת שקיפות' כדי לחשוף את רקע לוח המשבצות המציין אזורים שקופים.לאחר מכן, לחץ על חלון, ואחריו מעקב אחר תמונות בתפריט הנפתח כדי לפתוח את חלון מעקב אחר תמונות. תחת האפשרויות 'מעקב אחר תמונות', לחצו על 'קביעה מוגדרת מראש', לאחר מכן על 'סמל שחור-לבן', ולאחר מכן על 'מצב' ועל 'שחור-לבן'. לאחר מכן, תחת מאפיינים, בחר הרחב כדי להפוך אותו לווקטורי.בחרו בכלי הבחירה הישירה ולחצו על הרווח הלבן. מחק אותו, לחץ על File and Save As ובחר EPS To save as a vector graphic. ליצירת תבניות פיטופלנקטון, ראשית, צרו משטח יצירה חדש בסביבת עבודה חדשה בלחיצה על הכלי משטח יצירה מרובע בסרגל הכלים.צרו שלושה משטחי יצירה זהים באותו גודל באמצעות התאמת הגודל בתוך 'מאפיינים'. גררו ושחררו את קובצי EPS של טקסי הפיטופלנקטון השונים במשטח היצירה. השתמש בכלי הבחירה הישירה כדי לצייר תיבה סביב פיטופלנקטון בודד.תחת מאפיינים, בחר הטבע, ולאחר מכן מילוי, וצבע את הפיטופלנקטון בצבע הרצוי מתוך לוח הצבעים, המייצג את העשור. לאחר מכן השתמשו בכלי בחירת החץ השחור כדי להדגיש פיטופלנקטון מסוים. בחר ערוך, לאחר מכן העתק, ואחריו ערוך, ולחץ על הדבק.הדבק כל וקטור פיטופלנקטון באופן איכותי בהתבסס על הפרופורציות היחסיות של כל טקסה במערך הנתונים עבור כל אחד משלושת העשורים. בחרו 'עצם', לאחר מכן 'דוגמת מילוי' ו'צור' ליצירת דוגמת מילוי של דוגמית צבע מסוג פיטופלנקטון לכל אחד משלושת העשורים.

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Environment

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 ...