Image Analysis using "Sample Point" Software

Image Analysis of Percent Coverage using "Sample Point" Software

Our group analyzed percent coverage of vegetation for all quadrats within the 17 transects using free software called "sample point". Sample point software can be downloaded through the following website: http://samplepoint.org/index.html. Once the program is downloaded, go to "Options" and select "Database Wizard - Create DB" so that you can create a database name with the images you are wanting to analyze. Create a database name (example: Transect_1). Select "Create/Populate Database" chose the images and then select "Done". You can select more than one image for each database created. For instance, I selected all of the images that were located in one transect so that each image for all 5 quadrats within a transect were analyzed and stored in one excel spreadsheet. Go to "Options" and click on "Select Database". Chose the database you just created. If this is your first time using sample point, you will need to create buttons of the species you are going to be analyzing. Go to "Options" and highlight "Create Buttons" then select "Create Custom Button Files". It is best to abbreviate each of the species' name you are creating a button for because long names tend to get cut off. Save the custom button files once you have entered all of the species' names you will be analyzing. After you have created a database and created a custom button, you need to upload the button file to your database. Go to "Options" and highlight "Create Buttons" then select "Load Custom Button File". Chose the button file that you need. This has to be complete each time you create a new database. You can always create or edit your custom button's file if needed. Now you need to chose the grid size (points to be analyzed for each image). Go to "Options" and highlight "Select Grid Size" then chose the number of sample points. In our research project were used 64 points. Now you are ready to begin analyzing your data using sample point. Click on "Begin" to get started. You will need to zoom into the image until you see a red cross-hair cursor. Enter a zoom value from 1 to 12 and click "Refresh". Click on the species' button that the middle of the Red Cross-hair is positioned on. You can always click "Back" if you chose the incorrect species. Once you have selected species names for all of the grid points and you have exhausted all of the images, go to "Options" and select "Create Statistics Files". Using 64 sample points to analyze marsh vegetation, I was able to complete all 5 images for one transect in approximately 25 - 30 minutes. I believe that the percent coverage accuracy should increase with an increase in the number of sample points being used to analyze the images.   

Data Analysis and Preparation

Brian and Jesse 

Data Analysis and Preparation - November 23, 2013

Brian, Jesse, and I went to the library to work on our project after we spoke with Dr. Smith about how we should analyze our data. Jesse created a bar graph to represent the marsh-edge movement of the two control sites (north and south of the reef) and the restoration site (older northern section and newer southern section). Brian searched for a technique to determine if the two vegetation analysis methods were comparable. He found the Bland-Altman plot which can be used to determine if the different methods are interchangeable/comparable at estimating percent coverage. I worked at compiling our sample point data into one excel spreadsheet.

Day 3 - Marsh Vegetation Data Collection

Jason and Sharilyn analyzing vegetation behind the oyster restoration site

Day 3 - Marsh Vegetation Data Collection: November 16, 2013

Jason and Bryan

Brian, Bryan, Jason, Jesse, Dr. Smith, and I headed out to the restoration site to finish our final day of data collection. On our way to the restoration site, the GTMNERR mule broke down. Brian, Jason, Jesse, and I loaded our supplies onto the golf cart and rode to the restoration site while Bryan and Dr. Smith waited for help. The weather appeared to be better than the previous day, but as soon as we started collecting data another storm started heading in our direction. Bryan, Jason, and I took photographs and collected canopy height for the remaining 13 transects. Brian and Jesse collected measurements of the marsh-edge movement from previously marked quadrats in front of the marsh-edge. They also collected the remaining GPS coordinates for the end of the transects (16 m). Fortunately, with everyone's participation we were able to collect all of our data just in the nick of time before the storm arrived.

Brian and Jesse measuring change in marsh-edge

Day 2 - Marsh Vegetation Data Collection

Boat Generated Waves at the GTMNERR Restoration Site

Day 2 - Marsh Vegetation Data Collection: November 15, 2013

The weather seemed to be working against us on the second day of data collection, but Brian, Jason, and I were determined to accomplish the task we set-out to complete. We arrived at the restoration site early so that we would be ready once it was low tide. Unfortunately, we were only able to complete one whole transect (transect #4) because of the rain. Instead of returning to the GTMNERR Education Center and calling it a day, we changed our game plan. We decided to prepare for our third day of data collection (November 16th) by marking all of the five quadrats for transect 5 - 17 with yellow flags. I used this opportunity to get some really great photographs of the reef at low tide being bombarded by high energy waves generated by boats. The pictures illustrate how the oyster reefs protect the marsh vegetation by creating a barrier against the wave activity.

Brian marking the quadrats with yellow flags

Jason taking images of the marked quadrat

Day 1 - Marsh Vegetation Data Collection

Brian and Jesse analyzing vegetation using the visual method

 

Day 1 - Marsh Vegetation Data Collection: October 26, 2013

 

Previously Marked Quadrat

Our group decided to analyze marsh vegetation at three different locations adjacent to the Tolomato River: north and south of the restoration site (controls) and directly behind the oyster reef. Originally, we were going to analyze 25 transects positioned approximately 25 meters apart, but we decided to analyze 17 transects that were set-up behind previously marked positions by the GTMNERR staff. All transects contained five quadrats positioned at four meter intervals (0, 4, 8, 12, and 16). Each transect began at the edge of the shoreline where the vegetation started (0 meters) and ended 16 meters from the starting point.  One quadrat (1 m²) made from white PVC pipe sectioned into a 16 celled grid was to be placed around each area of interest on the transect. All of the original 25 transects were going to be analyzed using the visual method for determining the percent coverage of each species within the quadrats. However, Jason Lynn (biological scientist at GTMNERR) demonstrated a new technique for analyzing vegetation using photographic images taken directly above the marked quadrats. Percent coverage using the image analysis method was determined with free software called sample point.

Our group collected data on three transects using both the visual and image analysis method to see if they were comparable at determining vegetation percent coverage. We also collected and recorded the average canopy height of each species located within each quadrat.

Visual Analysis Method

The camera being positioned over the quadrat appeared to reduce errors that are generally made with the visual analysis method and decreased the time spent in the field. 

 

Jason collecting canopy height

Lessons Learned

This past Thursday was the poster presentation and I thought it was really neat to get to see everyone's finished projects and the results after so much hard work. It was very rewarding to see how the hard work has paid off and how we can contribute to the scientific community with our research even though we are all still undergrads. To me that is a really unique and captivating experience. That is one reason that I am thankful for this class. Another reason that I enjoyed this class was because it taught me how to be a scientist outside of the classroom. Most of the classes I take may have labs where we do some work in the field but the emphasis is always on what we are learning in the class room. This class reversed this and used the classroom time to emphasize the work we were doing out in the field. I enjoyed this fresh perspective especially since this is what I want to do in my career. This class has taught us how to take what we have learned in the classroom and apply it to real life situations and tests our ability to turn knowledge not into a grade but scientific results. I believe that this skill is invaluable to scientists seeing as much research is done in the field. This class also taught me several of the common methods of sampling used by researchers, such as seining, eckman sampling, transect sampling, collection trays, B traps and many more. We also learned how to collect and analyze water quality data. All of the hands on experiences that I have gathered from this class will definitely be useful later in my career. And for these reasons I am thankful for this class. 

Vegetation results

Our experiment yielded interesting results on the vegetation dispersal in the GTM NERR restoration site. We found that Spartina alterniflora was the most abundant along the shoreline while the smaller plants such as Batis maritima and Sporobulus virginicus dominated the more elevated regions. We postulated that because Spartina is very stress resistant it is able to thrive in these high stress environments. The Spartina also reduces the wave energy which we believe allows the smaller salt resistant plants able to grow behind the Spartina regions. However the results that we were mainly focusing on were not what we had expected. We thought the reefs would act as a wave buffer and make the areas behind them more stable which would allow for sediment accumulation and vegetation expansion. What the data showed was that there was no significant difference between the north site behind the reef and the control sites on either side of the reefs. This was the older section of the reef which was installed about a month prior to the south reefs installation. That is why we were surprised to see that the north section had lost more shoreline then the south section which had the oyster reefs for a shorter amount of time. This was the opposite of what we were expecting. To account for this we hypothesized that because of the reefs small size they may not prevent erosion but merely change the way that it occurs. To better understand our results further experimentation is required.

We reached the finish line

The end 

Throughout out the semester we learned the importance of restoration ecology and got to see and participate in projects relating to the restoration at GTMNERR.
The overall experience taught me a lot, I had never done a project like this or having to put a poster together. My group's project focused on fish assemblages and water quality comparison of a restored site with a non restored site.
I am glad I learned as much as I did and I hope in the future to participate in restoration projects. The importance of restoring habitats is huge, everyday we lose more habitat to human activity and  natural disasters and it is important to understand our impact and act to prevent permanent damage.
I want to thank the GTMNERR and the UNF Coastal Biology department for the assistance and use of of their resources. I am very exited that our posters will be shown at the 2014 GTMNERR State of the Reserve and that I will be able to spend some more time with the people I met and have built friendships with in this class.

Vegetation sample methods

One of the things that I found interesting as we analyzed the vegetation data that we collected was that the two methods of collecting data we compared were not interchangeable. We used a Bland-Altman plot to determine if they were comparable methods of collecting data and found many values that were out of the tolerance range, indicating that they are not equivalent methods of collecting data. However this plot does not tell which method is better for sampling, merely that they do not record similar data. This is essential because if the visual analysis is more accurate then using the sample point program then all of the that data we collected might not be very accurate or give us a good representation of what the area is actually like. This means that if another researcher uses this experiment as the basis of a further study they must also perform the same methods that we did and can not use the visual analysis method or their results will not be correlated to our research. One way that would could further examine the differences between these two sampling methods is we could do all 17 transect with both sampling methods. That way when further researchers come to use our data they will have two types of tests to determine whether the shoreline vegetation is actually changing or not. Doing this would lead to more accurate future data then just picking one method. However due to time constraints this was not possible and we must settle for only performing one method.

Bland-Altman graph of the visual vs the sample point methods. (Does not show several values far above the upper limit.)

This is it!

Today is the day! We will be presenting our projects in about an hour and a half and I could not be more excited/nervous. This is basically one of the last things we have to do, as our research paper is nearly complete. After we present today, and finish the paper of course, the only other thing that will be done with this initial phase of the study will be to meet with the friends of the reserve in February at a poster session outlining all the projects that have occurred at the GTM NERR in the past year. Honestly, I feel privileged to be able to present our findings in the spring, so I really can't wait. I would like the Guana Tolomato Matanzas Research Reserve for allowing us to use their site and some of their supplies (even those pesky mules that only wanted to work properly sometimes).
As well, I have been given the opportunity to continue this study in the spring, though in an independent manner. In doing this, I hope to continue to learn about restoration projects and the actual science behind it. Overall, this is a field I have a growing interest in and perhaps being able to continue to work in the field an actually apply what I have learned in the classroom will help me gain experience in what could be a career choice (though I do really need to get used to early morning events apparently!).
I really enjoyed this class and in saying that, I would like to thank Dr. Smith for being such a helpful and understandning profeesor and I look forward to working with her more in the Spring. As well, my group was awesome and I didn't ever feel affected by "Group Hate Syndrome" (which yes, its a real thing). . Everyone put together a collective effort to put this project together and I think we really did a great job. We spent countless hours in the lab and library trying to pull this project together and I honestly look forward to working with Najda and Collin more in the Spring as we work on our independent study.

Everyone at the Oyster Bagging Project

Dr. Smith showing us the restoration site for the first time

Dr. Smith teaching us about sediment analysis

Waiting to do seining

Working on our vegetation sampling

Finally, analyzing the fauna of our settlement trays

A little bit about the reserve and the importance of oyster reefs

Guana Tolomato Matanzas National Estuarine Research Reserve

Shannon and I with the bagged Oyster

According the the Friends of the GTM Reserve, "The Guana Peninsula along the Tolomato River has provided sufficient habitat for the eastern oyster,Crassostrea virginica, in the past." However, we have seen a decline in the abundance and density of oyster reefs in the area over the past few years by such anthropogenic means of over-harvesting, water pollution, increased river traffic, dredging, development of coastal zones, and climate change. This has caused erosion of the shoreline and a decline in vegetation. That being said, work has been done to try and restore some of the coastline and reduce shoreline erosion through the introduction of artificial oyster reefs. These reefs are made from recycled oysters from local restaurants. At the GTM NERR, over 1000 feet of shoreline has been restored. Some of these restoration techniques can be seen in this video by the reserve. In restoring these shorelines, they hope to successfully restore 0.76 acres of degraded saltmarsh habitat, .071 acres of oyster habitat and 1.16 acres of benthic habitat.

This is where we come in. 

Not only did we help out during an oyster bagging event, but we also started a 2-year regimen of testing the restored site for increased biodiversity both within the reef itself but also the sediment and shoreline surrounding. We also hope to see a decline of shoreline degradation and erosion. The Nature Conservancy actually does a fantastic job at explaining the purpose of these amazing oyster reefs as well as documenting some of the oyster reef restorations within the southeastern United States. Thet outline the problems faced with the degradation of the natural habitats, the amount of loss (nearly %80 worldwide) and what is being done to reverse this travesty. 

Oyster Reef Restoration: The American Southeast

The Amazing Oyster Reef

Everyone with the Oysters!

Continuation

This is a satellite image of the site at Guana Tolomato Matanzas National Estuarine Research Reserve with the location of the settlement trays and fiddler crab burrow transects in the restored and non-restored sites. I have received approval from Dr. Smith to continue in assisting with the research being conducted at Guana. I am honestly pretty excited to be given this opportunity and I hope I can add to the team. I believe this will be very beneficial in the coming years and will really allow me to focus on the skills that are required to operate in this field. It isn't very often you find a University offering a course with this experience, typically I feel like you have to find an internship for an opportunity like this. I will begin assistance in the Spring of 2014 and I will also be planning on using my research, or separate research, of this study or my own for my senior project. Estuary restoration is crucial for an area like North East Florida since it is a peninsula state and majority of the development occurs along the coast. As well as the role certain estuarine organisms play in maintaing the water quality by filtering out harmful chemicals and organisms. And I feel like our research is important on a number of levels from economical gain to aesthetic gain.    

The Poster, The End

This is the final product for the benthic group's project on abundance and biodiversity of bethic organisms at the site in Guana. We will present our data on 12/6/13 in the biology building at the University of North Florida. Today 12/5/13 we gathered and discussed how we were planning on presenting the data and finalizing our paper. It has been a long semester and we have logged numerous hours both in the field and in the lab. But I can say that this was an enjoyable class where you took the things you've read about, from the introduction of the major, and applied them in the field. It was very work intensive course and required a good amount of reading, all of which was supplemental to the skills you would be practicing in the field, but I feel like it was all worth it. I am very proud of my group, especially Nadja Capps she was definitely the team captain on this one. Also, a special thanks to the folks at Guana for letting us participate in their research and for letting us use their equipment and the site.

The Results

During the end of November the benthic group worked on analyzing our data and finalizing the results. Our results supported our original hypothesis in that the restored site had higher diversity and abundance when compared to the non-restored site at Guana. The settlement trays behind the restored site had a count of 1,033 individuals and only 866 individuals in the non-restored site. But the species richness was the same in both sites, with a count of 17 unique species in each.   

    The core samples from the restored site had a higher species abundance in oligochates, polychates, 

amphipods, and gastropods when compared to the species abundance in the non-restored site. Total 

species abundance for the restored site was approximately 479 individuals while in the non-restored 

site the species abundance was only 66 individuals. The restored site had a species richness of 4 

unique species, while the non-restored site had a species richness of 5 unique species. 

     From the shells recovered for oyster spat settlement in the restored site the mean count in the

 restored site on the vertical shells was 2.75 and on the horizontal shells was 3.5. In the non-restored 

site there was no data for the vertical shells since all of the shells were lost sometime during their two

week deployment, and on the horizontal shells the mean count was 6.25. In both sites the 

horizontally placed shells had a higher mean settlement of  oyster spat than shells that were vertically 

attached.

     The data from the transects of fiddler crab burrows show that a higher mean concentration of 

burrows were found closer to the shoreline behind the restored site between 0 and 4 meters, while 

behind the non-restored site a higher mean concentration of burrows were found between 4 and 8 m.

The Project is finally nearing its end

The Poster

Today we worked on finalizing the presentation for tomorrow. I am so excited to finally present the findings from all the hard work we put in, but at the same time I'm so nervous to see who else Dr. Smith has invited. I really like how our poster turned out and I think the pictures and graphs chosen really represent the goals and outcomes of our project well. We were able to use one of the diagrams I drew myself which I think is pretty cool. We were unable to find a diagram online and unfortunately didn't think to take a picture until after the fact. As well, I think the map of the sites really helps to represent the scope of our project on more of a landscape scale. If you look close enough you are actually able to see the restored reefs along the coast which really helps add an almost aesthetic value to the restored reefs. As well, the graphs really help to show the results in a clear manner. There were so many organisms we identified (well over 2000!) that if we tried to describe every species collected we would run out of room. Instead the table given summarizes data and shows clearly the results- the restored site had a higher abundance than the non-restored site. However another graph shows that fiddler crab burrows in the non-restored site were more abundant in the quadrats past 5 meters from the shore, which could contradict our hypothesis of finding greater diversity and abundance in the restored site. Overall, I think the poster is a great representation of the project and really highlights the main aspects of the project.

Finishing up the paper!

Working on the presentation!