Hi I'm Travis, plant scientist at UC Davis, and I'm pumped about plants and agriculture. I like practicing languages and meeting people from around the world.
If the drone methods are useful to you, please consider citing our paper:
Parker TA, Palkovic A, Gepts P (2020) Determining the Genetic Control of Common Bean Early-Growth Rate Using Unmanned Aerial Vehicles. Remote Sensing, 12:1748.
Thanks, this is helpful. My problem is that I can view the coordinates in the image properties details box, but I don't know how to use that to find a location on a map. The format doesn't seem to be any known type of latitude and longitude notation. If I copy it into the search bar of a map application it just gives an error.
@Travis Parker, Hi Travis, Could you please explain how to get DSM of plots? I have a drone image consisting of 7 bands (RGB, NIR, SWIR,...). Can I calculate/estimate plot volume in the absence of LIDAR data? If yes how?
I am not sure exactly what you mean, but pulling the time stamps from the EXIFs can honestly be really annoying. I was messing around with that in the command line a few months ago and it kept failing. I know there are some exif reader software options, but I remember stopping without pursuing it further at some point. Sorry to not be more helpful
I eat a lot of dry beans and prefer to grow them myself. A home breeding project to improve productivity of my favourites would be fun. Thanks for the idea. Also found your How to cross beans vid. Very useful.
How can one get in contact with you? Emails cannot be attached to the comments section. You seem to be such a cool enthusiastic person who has a zeal for vegetative world. I'd love to be your pen pal.
OMG Thank you. I’ve been looking all Over for data. I didn’t even know sweet potatoes flowered. Now I’m interested in collecting seeds and cross pollination
Actually I do not want that my runnerbeans cross polinate. Any ideas how to do it? Maybe how far appart should I plant them? And how to tell the insects that they are not allowed to cross polinate?
Hi, haha good questions! Runner beans are tricky... they are the only domesticated Phaseolus bean that will not self-pollinate, unless someone does it manually! The flowers of most other beans will self-pollinate in the absence of insects or people. So it will be tricky, sometimes we self-pollinate the runner beans by hand (this must be done in the greenhouse, where there are no insects). But to get seed, something needs to pollinate, and if you have many varieties in an area, the bees will move the pollen around! So I would say there isn't a clear distance that bees couldn't / wouldn't cross. You can self-pollinate if needed, otherwise, the further the better, if you don't want outcrossing!
I used '(Threshold < 0.5)' as denominator for sDSM. However, the sDSM values were higher than the cDSM. How to calculate canopy height in such case? The images were acquired from corn trials.
Hi, I would use the information tool (little "i" symbol) to click around your field at areas of interest to check on that. I also use median soil values, rather than averages, in case you have furrows. But that would be a very strange pattern to have soil higher than canopies, I would check everything very carefully. If the plants are truly tiny, maybe < 3 weeks old, they might be too small to display properly, otherwise I would just thoroughly check everything
I live in the north. I am interested in hybridizing sweet potatoes with their cold-hardier ipomoea cousins that are also tuber-producing: Ipomoea pandurata & Ipomoea leptophylla. Have you ever attempted such crosses, know if this has been attempted before, or know if anyone else is currently working on this? Thank you.
Hi Travis, awesome video; we did a flight with the M3M RTK and the output was a shrunk mosaic, it had all the elements on the field but they were smaller compared to satellite imagery, do you have any idea why can this happen? kind regards!
Were the images in the correct location? About what was the ratio or factor of shrinking? It could be an issue with reading in the geotags in the wrong coordinate system if it is a major deviation
Hi, Here is a source for the Excess Green Index, if you are interested: Woebbecke, D.M.; Meyer, G.E.; Von Bargen, K.; Mortensen, D.A. Color indices for weed identification under various soil, residue, and lighting conditions. Trans. ASAE 1995, 38, 259-269. I will also shamelessly advocate for our paper where we published this whole workflow, including the use of excess green! Parker, T. A., Palkovic, A., & Gepts, P. (2020). Determining the genetic control of common bean early-growth rate using unmanned aerial vehicles. Remote Sensing, 12(11), 1748.
I developed a software many years ago to do exactly this. GIS software is no longer an option when you get to the 1000s of plots. A field like show here would take just a couple of minutes with the custom software. For more complicated grids you could split it (and rejoin) at selected rows or columns. A key to a good fit is the transform/deformation type: I found bilinear is superior to projective.
We do this on thousands of plots regularly, but if the spacing is tight, it can be cumbersome to try to separate exactly, so I usually try to build a little extra spacing into the trials when possible, or just extract from the centers of canopies. If you have links to other helpful tools, let me know!
Ahh, eu lamento ouvir isso. Para nos, na estufa, e quase 95%. Talvez 90%. Mas no campo, e muito menos, nao e comun ter suceso no campo, faz muito quente. Eu tentaria num lugar sombroso e fresco (nao tao quente), funcionaria melhor
Thanks so much for this detailed video! I'm starting my bean breeding at home this year and this helped so much! I've actually purchased your southwest gold and red varieties and will be backcrossing a lot to add in the "pole" trait to increase yield per sqft. Your focus on culinary varieties helped me realize I should breed the tastiest first! Good point! This is one of the best videos I've seen for bean breeding, keep up the great work!
I am interested in how to use image processing information in regresión models. Do you have any githun project, paper or other kind of literature I can check?
Hi Travis, and thank you for sharing the method. I found your videos super interesting, and thanks for that. I tried to apply it on forest (area partly covered by forest), used grid 50X50m, but he "Mean Canopy Height (m)" for some grid cells got negative meaning. Cannot say why that happened so. Could the terrain be the reason for that? It is not flat and even. "Canopy volume," calculated using the Mean Canopy Height, also got the negative meaning in the same grid cells. Talking about the canopy volume, I have another question: when applied to forest area, what your call "canopy volume" it is actually forest stand volume (including space in between the trees), while canopy volume would be the volume of the upper part of trees (i.e. leaves), right? Did I get you correct? Thank you.
Hi, thanks for your comment. Yeah I don't go into a ton of detail about how to deal with complex terrain here, but one thing that helps is to use a grid of smaller polygons. If you are dealing with a deciduous forest where trees lose there leaves, the best thing to do is fly in winter (with ground control points) and then compare to summer when trees are leafy. Negative values mean that your canopy is on average lower than the forest floor or other non-canopy areas. As far as canopy volume vs. forest stand volume, that might be, I think it depends on the resolution of your orthomosaic, maybe among other things
Very helpful video, thank you. I’ve tried a couple of times to cross beans but was stymied because thought I could not find any pollen. I have done pea crosses and they’re relatively easy - no messy pistil curling and gobs of bright yellow pollen! I thought beans would be the same. Wrong! Keen to try again next bean season.
I’m guessing that the same or similar methods apply to Vigna species. I’m interested in crossing some cowpeas, though I’d have to do something about ants which are mad for the nectaries near the flower base!
Hi Travis! Thanks for the great tutorial for QGIS, I am a beginner of this, so I have no idea how do you get the threshold layer, 0 value layer, 1 value layer, can you tell me more about it? Thanks again!!
Hi, this is part of a larger playlist: ru-vid.com/video/%D0%B2%D0%B8%D0%B4%D0%B5%D0%BE-obRng3LLkRs.html Specifically, this video might be useful: ru-vid.com/video/%D0%B2%D0%B8%D0%B4%D0%B5%D0%BE-uklnnLmfN6U.html
Thanks for the useful video and informations. I would ask you please about processing images, is it the same way to process images got from an RTK drone, images got from a simple drone (without RTK), and images got from PPK method ? I wanna know the difference between processing images in the three cases. Thanks.
Usually by the time you have a mask layer, you are working with your vegetation index data to get the data you need, and aren't going back to the original RGB except maybe to make slides for a presentation or something. For presentation purposes, you can often just put your sDSM (soil digital surface model, see the plant height and canopy volume video in this playlist) on top of your RGB layer in the layer panel at bottom left. If you really need a masked RGB orthomosaic for some reason, you would probably have to use the raster calculator (as explained starting around 0:55 in this video) to calculate (RGBband / mask) for each of the bands, then merge the outputs again as explained in the final video in this video series. I hope that helps!
Hi, I usually don't want to cut my raster images up into large numbers of smaller images, usually it is more manageable to just extract data from each cell in the grid but keep a single raster. But here's something to try: 1. Open both the raster and vector files in QGIS. 2. Make sure that the vector file is in the same coordinate reference system (CRS) as the raster file. You can check this by right-clicking on the layer and selecting "Properties" > "General" > "Coordinate Reference System". 3. If the vector file is not in the correct CRS, you can change it by right-clicking on the layer and selecting "Set Layer CRS". 4. Select the raster layer and go to "Raster" > "Extraction" > "Clip Raster by Mask Layer". 5. In the "Clip Raster by Mask Layer" dialog, select the vector layer as the "Mask Layer". 6. If necessary, you can adjust the other settings, such as the output file format and the output extent. 7. Click "Run" to clip the raster file based on the vector grid. 8. The clipped raster layer will be added to the QGIS project, and you can view it in the Layers panel. 9. You can also save the clipped raster as a new file by right-clicking on the layer and selecting "Export" > "Save As". In the "Save Raster Layer As" dialog, choose the output file format and location, and click "Save".
