BenchBot V3.1 Image Collection Protocols and Checklist

Supplies

1. Batteries

   1. 1x Camera Battery

   2. 1x Flash Battery

   3. 4x Amiga Batteries with 4x Keys

2. Camera with Attached Lens (handle with care)

3. Flash

4. USB-A to USB-C Cable

5. Measuring Tape

6. Color Checker

7. Stool

1. Setup Bench Bot and Camera

1. Attach the camera and lens if separated.

2. Replace the battery in the camera if low. I have found that

3. Attach camera to the flash bracket. It is held in place by a screw and two washers. Try to align camera lens to parallel with the ground as best you can, and tighten as much as is reasonable. If the camera is too loose, it does not have a risk of falling but the BBot’s movement can jostle it and cause it to be pointed at an angle, which can lead to the amiga being in frame, pot edges being cut-off, etc. if this was not anticipated.

4. Attach the camera to the BBot bracket. The black triangle piece on the back of the flash bracket will slide into the piece toward the bottom of the BBot z-axis. Make sure to have a strong grip on the flash/camera and always have a hand below the camera. It can take a couple tries to properly hook it on (sometimes only one side will slide in), so you want to ensure you do not drop it.

5. Unscrew the cap on the BBot box USB port. At this point, you may attach the camera to the box via the USB-C to USB-A cable. If using a long cable, make sure it does not hang below the camera so that it does not get in any of the photos.

6. If there is a risk of rain or if it is a hot, sunny day, it is advisable to put a cover over the camera.

7. Place the four amiga batteries into the BBot. There is a battery slot above each wheel that they will slide into. Make sure it slides into the bench bot’s internal track, it can be easy to slide one of the sides on top the track instead of in it.

8. Once all batteries are inserted, you may put the keys into the battery. When turning from “Unlocked” to “Off”, a little peg will push out of the battery (on it’s bottom side) to enter a hole in the frame of the Amiga. If you cannot change the battery from “Unlocked,” then it is likely the peg cannot extend down into the hole due to a misalignment. You may just have to wiggle the battery around a little bit, or the battery may not be in the tracks and you may have to slide it out and slide it back in properly.

9. Plug the dangling power cables into their batteries. Each battery has its own power cable.

10. Turn on the batteries with the key.

11. At this point BBot will begin booting up. The Amiga interface will be immediately available to use, while the BBot app interface will take a minute or two to boot. Remove the cover from the amiga interface, and press start. Reduce the motor speed to 4 bars (a value of 80). We do not want to BBot moving too fast.

12. Adjust the BBot alignment if needed using the joystick. At MD, the bench itself is a little curved so it can be difficult to get a straight alignment. Try your best to get the BBot wheels to be as parallel as you can with the left and right edges of the pots. It is okay to pause the BBot when it is running to make quick alignment adjustments later when you are conducting the batch collection. When choosing a starting place, make sure the camera is above the first row.

13. On the Amiga interface, click the “Auto” tab on the left (it is an A surrounded by a circle). On this page, turn auto-control on. The light on the joystick should be orange or blue. When this is on, the BBot will be able to control itself (so the Y-axis is now controlled), but the joystick will be unresponsive. To make further BBot adjustments with the joystick, you may turn this off when needed. Make sure to turn back on after making your adjustments, however, because if BBot is started with this “off,” then it will be unable to move forward and will continuously take images of the same row.

2. Thin and Weed Potting Area

Discard non-target weeds or overlapping plants by pulling them, shaking off their soil, and placing them into a bucket or bag. Do not leave removed weeds or plants on pots or on the landscape fabric. This is to avoid detecting them in the images that we collect.

1. Remove overlapping target weeds in all pots

2. Remove non-target weeds from pots and from the background area

   1. Check inside the pots for non-target weeds

   2. Check and remove weeds growing from underneath the pots

   3. Check for and remove weeds growing on the landscape fabric

3. Check Camera and Flash Settings

Make sure that the camera settings match what is listed in the camera settings table

1. Check aperture is correct

2. Check that the focus is correct

3. Check the flash power

4. Check height of the lens from the potting soil surface using a measuring tape

5. Place the color checker in frame of the starting position

6. Open the BBot app on the BBot interface and press the “take image” button to take a test image.

Camera and Flash Settings Table

4. Check and Adjust BBot App Settings

1. To avoid the Amiga/BBot frame being in the images, we start the camera at a position further in the X-axis, away from its right/leftmost position, which I am referring to as “0”. To get the camera into proper position, move the camera to the “0” position so that it is at its standard starting place, and then move it whatever distance your site species in the table below (the “x-axis starting” column).

2. If you are changing your species map (or need to replace it, as sometimes it will clear itself when restarting the app or BBot), use the “Species Map” tab to build it. Use the information in the table corresponding to your site to build the species map. At the moment, what you select for the “species” itself does not matter (we do not use that metadata and there are limited options). Just make sure to select a species from the list. If you leave it as “none”, BBot will not take images there. After making your settings, click add rows and your map will appear on the right side of the screen. If it looks good to you, then press “Save.” If you do not press save, then the map will not appear in the “Traversal” tab and you will have to rebuild it.

BenchBot App Programmed settings table

5. Begin the Batch

1. Start BBot collection via the “run” button on the “Traversal” tab

2. Stick around for at least the first two rows to ensure everything is working properly. If the BBot is not rolling forward after a row, then the auto button on the Amiga interface is likely in the wrong state (the joystick light should be blue or orange, not white).

3. Move the color checker, once it will no longer be in anymore images, to a new spot ahead of the BBot. I personally put it at the start of every species. It is good to have the color checker in a batch several times, as lighting conditions do change throughout the day.

4. Every now and then, when BBot reaches the ends of a row, check these outermost photos to make sure the pot is fully in the frame and no Amiga is in frame. If either of these happened, then your camera may not be parallel to the ground, or you may need to adjust BBot’s position with the joystick.

5. Depending on site, you may have to replace the flash battery every once and a while.

   1. At MD, our BBot does not charge the flash as it goes along, so the battery is not gaining any charge. I find that the Battery lasts about 2.5 species normally, so I like to change it out at the end of the second species and the end of the fourth species. Make sure to pause the BBot traversal before doing so, and also when you slip the new battery in, turn the flash on. The flash does not automatically turn on (even if it was still on when your removed the old battery), so you will have to manually turn it on again. Always have your flash batteries charging in case you are ready at any moment.

6. Packing-Up

1. Return BBot to its starting position.

2. Unplug the camera cable, and screw the USB-port cap back onto the BBot box.

3. Take the camera off the BBot. At the triangle mounting spot, there is a little tab you will need to press in to disengage the mount. When holding that tab in, you will be able to lift the camera/flash out. I like to have one hand dedicated to the tab, and another below the flash, holding it and pushing up.

4. Pack away any accessories you brought out (Color Checker, Tweezers, etc.).

5. Turn off Amiga batteries and unplug them.

6. Bring everything inside, and charge all batteries so that they are ready for the next batch collection.

7. Trouble Shooting Issues

Basic Troubleshooting Tips:

• Reboot BBot

• Check that the emergency breaks (red buttons on the yellow square) aren’t active. They should be lifted so that you can see a strip of black below them, indicating the brakes are not on.

• Check that you have a connection to Wifi. On the BBot interface, there will be a Wifi signal icon in the top right corner of the screen. Advanced Wifi settings can be looked at in settings if there is no signal.

• Check Amiga settings are properly set.

• Check that camera and flash are turned on, and plugged into the BBot.

If you are receiving “Missing JPG/RAW”, “Missing JPG”, or image always loading issues, we believe this is caused by an issue with the camera having a proper connection to BBot. Steps you can take to try to remedy this:

• Unplugging the camera cable from both ports several times. Try to image after each attempt.

• Dismounting the camera and moving it a little bit. Take its battery out, put it back in, etc. Doing anything to maybe jostle something back into place.

• Rebooting BBot.

If BBot starts taking images in the same spot and seems unable to move (both X-Axis and Y-Axis motors), I have had success just restarting the BBot app with that every time. Just close the app and reopen it.

Examples of Plant Spacing and Non-Target Weeds

Non-target weeds

Plant spacing

Avoid overlapping plants. Thin plants when they do overlap. Be liberal when thinning plants. We don’t need to worry about having enough plants. It’s more important to have no overlap than it is to have more plants per plot.

Prioritize no-overlap for plant within a pot and no-overlap of plants from different pots. View below for examples of good plant spacing.

Within-Pot Plant Spacing

Between-Pot Plant Spacing