Optical Dendrometry¶
You will need
A cavicam that has completed the setup procedure. See Getting Started section for more information.
A computer with wifi capability e.g. a laptop.
Step 1 - Access the caviconsole¶
See Accessing the Caviconsole for instructions.
Step 2 - Set to Dendrometry Mode¶
From the Capture tab, set the Mode to Dendrometry and click Update as required to save the change.
Note
For every settings change in the caviconsole, click the Update button after making the change.
Step 3 - Setup the Lights¶
Dendrometry involves backlighting the sample with the bottom light to cast the sample in shadow. Depending on how the wires were connected, Light 1 or Light 2 might be the bottom light, so we’ll first need to work out which one is which.
In dendrometry mode, the caviconsole provides two options for lights: the bottom light and the preview light. The bottom light is the one we always set as the true bottom light while the preview light we can set as either. The preview light is the light that’s used for the live preview and it’s often useful to use the top (overhead) light for sample positioning. Some prefere the preview light to be the bottom light as well so it’s closer to the final image - hence all the lights options.
Determine the bottom light¶
Click the Light button to toggle the light ON and watch the cavicam to see which is the corresponding light. For example, if the Preview Light setting is Light 1 and the top light comes on when you toggle the light switch, we know that Light 0 is the bottom light and we should set the bottom light option to Light 0… and vice versa. Remember to click the Update button after every light change.
Warning
There is a known bug in the caviconsole where the light button doesn’t honor the first light setting and will only update after the first round of changes. To get around this, just run through the procedure a couple of times, making sure the light is changing when you change the preview light setting.
Step 4 - Attach the Cavicam to the Sample¶
Loosen the grub screw on the collar and remove the camera assembly so that you can see inside the imaging chamber. Loosen - or completely remove - the side wingnuts so that the sample can be inserted between the top and bottom plates. Use the imaging chamber to position the sample and then tighten the side wingnuts to secure the sample in position. The sample should be positioned as close to the centre of the backlit area as possible.
Careful not to overtighten and damage the sample.
Step 5 - Open Live Preview¶
From the Capture tab, set the Preview light to the bottom light (don’t forget to click the Update button if you make a change) and click the Live Preview button to access a live feed from the camera.
In the live preview popup window, click Start Streaming to view the camera stream. Click the Light button to toggle the light on and off while streaming. If the light you expect isn’t turning on, run through Step 3 again.
Can’t see a live stream?
If a broken image icon appears instead of the live stream, something is wrong with the camera. Usually this is because the camera ribbon cable connectors are not correctly connected. Check that the orientation of the silver connectors is correct and that the cable is fully inserted into the connector and locked in place with the hinge/clip. Check the Getting Started section for more information.
Step 6 - Focus¶
Re-attach the camera assembly and while watching the live preview, move the camera assembly up/down to focus and rotate left and right to align the sample vertically or horizontally (rather than diagonally). Pay special attention to the edges of the sample (red arrows) and get them in as sharp a focus as possible.
Click the Stop button to stop streaming from the camera and toggle the light off by clicking the Light button.
Step 8 - Define ROI¶
From the Capture tab, click the Define Region button, wait for a preview to be generated.
Has it crashed?
The Define Region function captures a full size picture of the sample and this can take a while to load in the browser. In some situations expect to wait up to a minute for the image to load.
Once the image has loaded, click-drag (same action as highlighting text) to draw an ROI (green rectangle) around the sample as shown, covering the full width of the sample and approximately a third of the visible length. Ensure the background in the ROI does not include any dark areas otherwise these areas might be included in the measurement.
Step 9 - Set Shutterspeed¶
In most cases the default shutterspeed setting will work for most samples. If the sample is not in dark enough shadow, close the ROI window, decrease the shutterspeed (by 100 is good start) and click the Define Region button again to generate a new picture using the new shutterspeed setting. Continue this process until an optimal setup is achieved - the goal is enough of a separation in brightness between the foreground (the sample) and the background so that all of the sample can be separated from the background using thresholding. Light bleading around the edge of a petiole might exclude that area from the measurement, but in some cases it is unavoidable.
Step 10 - Set Sequence Name, Storage and Resolution¶
Sequence Name¶
Set an appropriate sequence name. This will be the name of the folder that stores the images and data for the sequence.
Tip
Incorporating the date into the sequence name can be useful for differentiating between sequences and can help with storage management e.g. Eucalyptus_29072021
Storage¶
Store data on the MicroSD card¶
Choose an option for the Output Directory. To store images and data on the Pi (on the MicroSD card) use the /home/pi/captures option.
Store data on an external USB memory stick¶
Choose the USB Stick option to store images and data on an external USB stick. Ensure that a USB stick is inserted into one of the USB ports.
Important note on USB sticks
USB sticks must be formatted in an appropriate format for the Raspbery Pi. See USB Stick Formatting for instructions.
Image Resolution¶
Choose the resolution for images. For optical dendrometry, leave the resolution at the highest setting.
Step 11 - Set the Pi Time¶
The Pi doesn’t keep time when turned off so the current time must be updated every time the Pi is turned on and before capture.
From the Util or Capture tabs click the Sync button to set the Pi time using the time on your computer.
Step 12 - Start Capturing!¶
Click the Start button on the Capture tab to initiate image capture.
Use the View Log button to check for issues and errors.
View the data live¶
Click the Dendro tab to see a live feed of the data. The plot shows area (number of pixels) of the sample in the ROI.
Download the data using the Download CSV button.
Columns are timestamp, width (pixels, ignore), width (microns), area (pixels), ROI height (pixels), ROI width (pixels).
Ignore width columns - will be removed in later versions.
Next Steps¶
Check out the user guide for accessing the images and data.
Check out the user guide for restarting after error.