TITLE: Post Processing: Abundance and Distribution of Species in Open Vegetation Plots
AUTHORS: Sabine St-Jean

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Here we describe the standardised protocol used by the </span><a href="http://www.caboscience.org/" style = "text-decoration:underline;color:blue;cursor:pointer;"><span style = ":;">Canadian Airborne Biodiversity Observatory</span></a><span> (CABO) to obtain an estimation of the abundance and distribution of plant species surveyed in the open vegetation plots in sites where small drone pictures are taken using the DJI Mavic Air, being Mer Bleue Bog (Ontario) and Parc national des Îles-de-Boucherville (Québec) in 2019. The </span><span style = "font-style:italic;">SamplePoint </span><span>program is used to process the small drone pictures, where a virtual point frame grid is overlapped to the subplot pictures. The grid is made of 100 crosshairs, representing one crosshair every 10 cm. Every crosshair is then associated to a ground cover. This process results in an Excel spreadsheet where we can extract a percent cover for each species (measure of abundance), and see for each of the 100 crosshairs per subplot what percent cover is present (measure of distribution).</span></div></div>

[STEPS]
?. [Photo Annotations]
If the different species are difficult to tell apart visually, annotate the drone pictures.
?. [Photo Annotations]
From Fulcrum, download on your computer the small drone pictures from the 9 subplots of a given plot by following Vegetation Surveys: Herbs and Shrubs → Cover Estimates: Subplots → Subplots → Record [# from 1 to 9] → Vegetation Photos: Subplot → Download → Original.
?. [Photo Annotations]
Open the 9 pictures in a single PowerPoint file, with each slide corresponding to one subplot.
?. [Photo Annotations]
Use the species list from Fulcrum → Vegetation Surveys: Herbs and Shrubs → Subplot Record → Cover Estimates to locate each plant species, paying attention to the Canopy Remarks (abundance and distribution).
?. [Photo Annotations]
For all of the species or specimens that are difficult to identify at first sight, in PowerPoint, in a white font, note the intials of the species (generally, format is first letter of genra + first letter of species) on top of its occurences.
?. [Photo Annotations]
Save all PowerPoint slides (1 slide = 1 subplot) in .tif to your computer and name them in the format PlotNo.SubplotNo.
?. [Virtual Point Framing]
Classify 100 non-random crosshairs per subplot using the SamplePoint program, in order to obtain species distribution and abundance to the closest percent.
Save everything related to SamplePoint (photos to classify (see 1.7), databases (see 2.2) and buttons (see 2.8) that will be created) in the same computer directory.
?. [Virtual Point Framing]
Indicate in the Veg_Crew_overview Google Doc on what plot(s) you will be working on that day, by writing the date and your initial next to the plot number.
?. [Virtual Point Framing]
Create a Database in SamplePoint, under Options ⟶ Database Wizard - Create DB.
We are using one database per plot, and only later combining all the databases into one.
?. [Virtual Point Framing]
Name the database with an acronym for the site and the plot number.
Boucherville: BOU#Mer Bleue: MB#
?. [Virtual Point Framing]
Populate the database by selecting all 9 annotated .tiff or .tif pictures of this plot.
Select All files from the menu in order to have access to the .tiff and .tif files.
?. [Virtual Point Framing]
Select Done and OK to complete.
?. [Virtual Point Framing]
Follow Options ⟶ Select DataBase, and select the file that you want to fill, then OK to open your database in SamplePoint.
Warning: if you select a database that has already been used, you will overwrite your data. Therefore we are using one separate database per plot.
?. [Virtual Point Framing]
Create, upload or edit a SamplePoint button file for classifying the plot.For every plot, using the plot species list in Fulcrum, under Vegetation Surveys: Herbs and Shrubs ⟶ [Appropriate plot] ⟶ Species List, all the species* must appear as a button in SamplePoint.
SamplePoint allows for a maximum of 30 classification buttons.  *: If there are more than 30 species in your list, add a button named Other that you will edit appropriately afterwards in the plot Excel Database. Make notes of the species of these Other-classified points in each subplot where they occur. Always include one button named Unknown, used for when you are not sure of the plant ID (for ex.: because of shade). If necessary, add buttons named Ground or Water. If necessary, add a button named Dry for cases where a plant is unidentifiable because only a dry stem remains.
?. [Virtual Point Framing]
Create a new set of buttons in SamplePoint by following Options ⟶ Custom Buttons ⟶ Create Custom Button Files.
?. [Virtual Point Framing]
Fill in the button names (4 letters, see buttons_explanations joined file) and descriptions (latin or common name; no single quotation marks) for every ground cover that will be used (ex.: species, bare ground, water, unknown, or other).
?. [Virtual Point Framing]
If a set of buttons already exists for the site, use it as a base to create this new set by clicking on Load Existing. Make the required edits by renaming the appropriate button names and descriptions.
The original button file will remain intact if the new one is given a new name.
?. [Virtual Point Framing]
Save and name this new custom button file.
?. [Virtual Point Framing]
In SamplePoint, follow Options ⟶ Custom Buttons ⟶ Load Custom Button File to select and load the buttons that you will be using to classify the photos from your database.
The Button File selected needs to remain untouched for the whole database.
?. [Virtual Point Framing]
Edit the picture as needed. The rotation has to be done once only, before classification. The rest can be done at any point and undone by clicking on R.
Use the buttons on the left menu to Rotate*, Darken, Lighten, reset (R), increase contrast (>> Cont), or lower contrast (Key indicates the Subplot number.Leave Block Zoom ticked. Only untick it if your computer performances are slow.*: Use the subplot number (title of the picture) and compare the picture in SamplePoint to its copy in Fulcrum** to know what rotation is needed.**: Especially useful for subplot no. 5.
?. [Virtual Point Framing]
Under Options ⟶ Select Grid Size, select 10x10 = 100. This means that we are using a 10x10 grid of points (100 crosshairs) to classify each subplot.
?. [Virtual Point Framing]
Click on Begin to start classifying. The 100 crosshairs are now regularly placed on the image, and one crosshair at a time (the red one) will be activated. To classify it, click on one of the 30 buttons of the lower menu.
The meaning of each button is indicated in the joined buttons_explanations Excel file.
The Zoom can be adjusted by rotating the wheel of a wheel mouse.
The Point field indicates the point (#/100) you are currently classifying.
The Back button is used to correct a previous crosshair classification.
?. [Virtual Point Framing]
To classify each crosshair, help yourself by opening (ideally on a different monitor) the Fulcrum Vegetation Survey: Herbs and Shrubs of that specific plot. Before starting to work on each subplot, open in two different tabs 1) the species list for the subplot and 2) the Original picture (not annotated) of that subplot.
Compare the Fulcrum species list to the annotated picture on SamplePoint to locate where the different species are. Use the zoom in the Original picture, as well and the Lighten, Darken, and contrast options in SamplePoint to help identify less obvious plants.
?. [Virtual Point Framing]
When the 100 points of an image have been classified, click on Next Image, then Begin to start again for the next image (= key = subplot).
You can stop working on a plot at any time (at the end of a plot, at the end of a subplot, or through a subplot) by clicking on the Exit button in the lower right corner of the screen. Make a note of the point where you stopped.To start back where you left, click Next image on the top menu until you reach the desired image. Then, enter the number of the point in the point field in the left menu and hit RST (restart).
?. [Data Combining]
Species that occur within the Fulcrum subplot species list BUT that are not observed by the point frame are assigned an abundance value of 0.5% in the Excel spreadsheet to account for their presence.
The last column (no. of species per subplot) of the table generated at step 5 is useful to compare your data to the Fulcrum records, when looking for absent species. Ground covers that are not species should be left out of the count.
?. [Data Combining]
Combine all the databases into one. Keep the originals as a backup.
?. [Photo Annotations]
Crop all photos so that their shape is a tight square around the PVC pipes delimiting the subplot.Example for subplot 1:
?. [Photo Annotations]
Save the cropped photos back to:1) their original Fulcrum subplot record, under Vegetation Surveys: Herbs and Shrubs → Subplots → Record [# from 1 to 9] → Vegetation Photos: Subplot,or 2) to a Google Photos folder, with all photos labelled with PlotNo.SubplotNo, shared with the Veg Crew Leader.
?. [Data Combining]
In Excel, create a final table to calculate the percent cover (abundance) of each species in each subplot. The subplot numbers are now used as the top row, and the species button names as the left column. In each new cell, write the formula =COUNTIF(E$12:CZ$12, C23)where E$12:CZ$12 is the list of the 100 buttons for the given subplot, and C23 is the name Excel is searching for.  The value that will appear in the new cell is the relative abundance of the given species in the given subplot.  At the end of the table, add one row to calculate the sum of the relative abundances. The sum should be of 100.  Add one last row under the previous one, containing the number of species per subplot. The formula to enter is where E$12:CZ$12 is the list of the 100 buttons for the given subplot, and C23 is the name Excel is searching for.The value that will appear in the new cell is the relative abundance of the given species in the given subplot.  At the end of the table, add one row to calculate the sum of the relative abundances. The sum should be of 100.  Add one last row under the previous one, containing the number of species per subplot. The formula to enter is At the end of the table, add one row to calculate the sum of the relative abundances. The sum should be of 100.  Add one last row under the previous one, containing the number of species per subplot. The formula to enter is =COUNTIF(D22:D62, ">0")where the cells D22:D62 are the percent cover values across all species within the subplot, and >0 accounts for presence.
?. [Data Combining]
In Excel, create another version of the existing species per dot per subplot table, that doesn't contain the RGB values. To do so, copy the name of the image column and the point numbers row. Then, for a given point * subplot cell, write the formula =LEFT(E3,4). This new table must contain 900 cells (100 points * 9 subplots).E3 being the name of the original cell, and 4 being the amount of characters kept, starting from the left.