Plant Tracer Web App Tutorial

Welcome and Registration

• If this is your first time using Plant Tracer, you will need to register for an account, unless your course administrator has registered an account for you in advance. To register:

• Go to prod.planttracer.com/register.

• Register for an account using your Name, Email Address, and Course Key.

• If you are using Plant Tracer with a specific course or project, you can enter your course Key provided by your course administrator (your instructor should be able to help you here).

• Alternately, you can register for the Web course whose course key is 2c01-48cd

• Once you are registered, look for an email from admin@planttracer.com. Click the Log in to Plant Tracer button to log in. From there you can upload movies or view a list of existing movies to work with.

Viewing movies

• Click on “Movies” in the menu bar at the top of the page to see a list of movies to analyze.

• Click on the analyze button to see the tracked movie.

Uploading Movies (optional)

• Ensure that your video is of a size that works well with Plant Tracer. You may have to resize it before uploading, either by trimming its length or reducing its resolution. The movement tracking algorithm(s) Plant Tracer use(s) actually work better with fairly low resolution, so no need to be concerned about losing any detail. We recommend a frame size of no more than 640 pixels in either dimension. We recommend a maxiumum of 1,000 frames per movie, though we permit a maximum of 10,000 frames. Your movie file must be 256MB or less or you won’t be able to upload it all. Plant Tracer will automatically resize (downsample) uploaded movies to a width of 640 pixels, if the movies have a resolution higher than that. See Resizing Video Files for some ways to resize videos.

• Plant Tracer will accept videos in most well-known video file formats, but MP4 is probably best.

• To upload your movie, select Upload from the menu bar at the top of the browser frame.

• Enter the title of the file and a description of the movie.

• The upload form asks whether your movie may be used in academic research. Before answering, review the Contributor Agreement linked on the form. Select Yes or No. If you select Yes, you will also be asked whether you want to be credited by name; your display name is pre-filled as the attribution name, which you can edit.

• Choose a file to upload.

Tracking the Uploaded Movie

• Once the file is uploaded, the page shows a first frame of your movie and a “Next steps” section. Click Analyze to go to the Analyze page. (The Track the uploaded movie link goes to the same place.)

• There’s an opportunity to rotate the movie 90° clockwise as many times as necessary to orient the movie properly if it’s not. Note that once you proceed to the Analyze page, you won’t be able to rotate the movie anymore.

• On the Analyze page, position the markers (described below), then click Trace movie to begin tracking.

• Plant Tracer places three markers on newly uploaded movies automatically. They initially appear on the left side of the movie frame. These also appear in the Marker Table to the right (or beneath) the video frame.

• Plant Tracer will attempt to track the motion of whatever part of the image a marker is placed over, frame by frame.

• It is the user’s job to position the markers appropriately. To move a marker, click on it, and drag it to the desired location.

• You may use the Marker Table to add and delete markers. There may be any number of markers. Markers cannot be renamed; to use a different name, delete the marker and add a new one with the desired name.

• Plant Tracer will attempt to track the motion related to every marker.

• Typically, the apex of some part of the plant is tracked. So, to do that, move the Apex marker, for example, to the top of the vertical stem.

• Markers whose names have the form RulerXXmm are special. XX is any non-negative integer representing a real-world distance in millimeters. These markers are used for distance calibration. The value of XX must match the actual ruler markings in your video — for example, if your ruler is 30mm long, you need markers named Ruler 0mm and Ruler 30mm, not Ruler 10mm. The default markers are named Ruler 0mm and Ruler 10mm; if your ruler uses different values, delete the default marker and add a new one with the correct name (e.g. Ruler 30mm) using the Marker Table. In this way, Plant Tracer can report analysis results in millimeters rather than pixels.

• There can be any number of RulerXXmm markers, but Plant Tracer will only use the RulerXXmm markers with the lowest and highest XX values in its calculations, and ignores any intermediate RulerXXmm markers for purposes of distance calculations. Plant Tracer only uses mm distances.

• If there are fewer than two RulerXXmm markers on a given analysis, then analysis results are calclulated and presented using units of pixels.

• The Apex and ruler markers need to be moved to the appropriate location.

Viewing the trace of a Movie

• Once the tracked movie has loaded you will see the image of the first frame, the marker table and graphs of the tracked movement.

• Click on the play button to view the movement of the apex in all frames of the movie.

Interpreting and Reading Results

• Use the arrow buttons just below the tracked movie to play, or navigate to a particular frame.

• The Position Graphs visualize the change in the non-RulerXX markers’horizontal (x position) and vertical (y position) since frame 0.

• When tracking is complete, you can press the “Download Trackpoints” button to get the tracking data in CSV format.

• At this point, you are ready to use a spreadsheet to further analyze and graph the data.

Further Adjustments to Tracking

• You can enlarge the image of the movie to better view the markers and tracing.

• You have the option of re-tracking the movie from that frame.

• Use the arrow buttons just below the original movie to navigate to the frame where tracking was lost.

• Then move the apex marker to the correct position. Now press the button “re-track movie”.

Converting Frames to Time

Currently, the Plant Tracer webapp tracks time only as frame numbers in the uploaded movie file. It is up to the the user to convert frames to elapsed timestamps from the beginning of the video. When recording the movie, the frame period was set: you must know what that was. In Lapse-It, this is one of the parameters set for the recording. Typically, the frame period is one frame every two minutes (120 seconds) or 30 frames per hour.

To convert frame numbers to time, multiply the frame number by the frame period:

• t[n] = n * FP

For example if the period FP = 2 minutes, then:

• t[0] = 0 * 2 minutes = 0 minutes

• t[1] = 1 * 2 minutes = 2 minutes

• t[2] = 2 * 2 minutes = 4 minutes

• etc.

If you have a frame rate (frames per unit of time) rather than a frame period, the frame rate is just the inverse of the period. If the frame period is 2 seconds, the frame rate is 1 frame/2 seconds or 0.5 frames/second.

Let FR be the frame rate. The time t[n] at frame[n] is therefore (n * (1/FR)).

For example, if FR = 0.5, then:

• t[0] = 0 * 1/0.5 = 0 seconds

• t[1] = 1 * 1/0.5 = 2 seconds

• t[2] = 2 * 1/0.5 = 4 seconds

• etc.