April 16, 2019
April 9, 2019
Alright, so, we are just about a full house here already. So, we’ll get started with the presentation. As you should be able to see on your screen, it should say, “A Change of View: Using Root Imaging to Expand your Research by CID Bio-Science.” Online with me is actually our distribution manager, Suzy Truitt. She’ll be helping in the background facilitating with the Q & A as well as the overall structure and architecture of this webinar. As you’re an attendee using the Zoom software, I just want to give you a couple tidbits. If you like go down and it won’t show up immediately but when you scroll all the way down to the bottom of your screen, you’ll see a bar pop up and it should give you options like chat, questions and answer, as well as raise your hand if you’d like.
So, I’m going to give the entire presentation and a short video for this webinar but at the end of it we’re going to leave plenty of time for questions and answers—any questions, please put them in that Q & A box and we’ll be getting to them towards the end. Now, this webinar is being recorded, so, if you have anything you’d like to see later on, if you’d like to come back to it we’ll be able to share this later as well as if any of your colleagues need the information as well.
So, to get started—if I can. We’ll be covering the CI-600 and CI-602. Now the 600 has actually been around for about 10 years and it is an In-Situ Root Imager and the 602 has just been developed as of last year using more recent technologies, being able to diminish the size of the root imager but still keep it so that it can be applicable out in the field in already established tubes. But first, let’s cover, why should we study the roots? One, I mean, it’s a critical success for the whole plant. They are absolutely critical for understanding plant or crop yield, environmental effects, the additions of certain chemicals and elements, and greater emphasis has been placed on root study that no longer instruments such as the minirhizotron simply in the domain of scientists, but they’re also being utilized by crop consultants, agricultural researchers, farmers, to understand the effectiveness of like soil treatment, fertilizers, and other nutrient applications. They be able to be used for, say, measuring and planning for the impact of drought and temperature fluctuations or monitoring for root pathogens and estimating crop yield. So, root study it’s just an intricate portion of understanding the plant’s health and production as a whole.
So, getting back to root study, a lot of studies are very much actually destructive of the roots, which really kind of has a hard effect to being able to visualize the roots in their natural biome, do a non-destructive assessment and see how they grow and being able to do it repeated over time assessment of, of course, growth, application studies and pathogens. So, since the proposal by the J.H. Bates back in 1937, minirhizotrons have been constructed with a kind of a successive list of technologies starting down with just mirrors in order to visualize roots and provide means to non-destructively repeatedly assess root conditions. So, minirhizotrons have been utilized to study, again plant response to drought conditions, compare treatments over time—my personal favorite, map phenotypes and genotypes, and overall find correlations between below ground characteristics and above ground function.
However, minirhizotrons in the past had some major historical setbacks and in fact, even the rhizotrons that they came from, which were originally just very large boxes, you would actually be able to walk into and have glass walls, have some issues you would have to deal with including restricted accuracy, low image quality, limited size and I’d also like to put in here, very hard to replicate a very similar environment when you’re allowing in other environmental factors like UV light. The great thing about modern systems, especially with the CI-600 and the CI-602, is that it’s lightweight and portable. It’s ideal for remote locations, you can use root tubes, glass or acrylic, and they have variable DPIs, so, like the stops per inch and that’s just the resolution levels, which you’re scanning so that you can do very quick scans at low resolution getting your information or you can do more intensive scans at higher resolution, so you can see things all the way down to root hairs mycorrhizae.
So, the CI-600, to answer a lot of the problems that minirhizotrons have had in the past we developed this over 10 years ago. It’s portable, scanner-based. As you can see in the tube, the scanner is just attached to a sliding rod as well as a computer which is off screen and the tablet computer, with that you could just press go and you can scan 100, 300, or 600 DPI. Using both the cap and the sliding rods, you’re able to measure, as you go down the tube visibly, so you know how many scans you’re at. And the great thing with using technology like this is that you can do one scan at one level, slide it on down at a measured rate, do another scan at a different depth and then later on at our root snap software you can actually take these scans and put them together to make an overall, large picture of the root system that you’re looking at in that location. We also actually provide, when we do give out the CI-600, we actually provide six acrylic tubes including with—as you can see here, actually clear and we will be talking a little bit more on that later on. We also provide them singularly as well if you already have a CI-600 or 602, we’d be able to get those for you.
The 602 advancement, it’s two inches in diameter as opposed to the five. Also, water tight and insulated. The two inches actually fits into some existing insulation for some older minirhizotron systems. It’s a little bit higher speed, so, we’re actually able to get scans at a hundred, 300, 600 and 1200 DPI which has been actually really interesting effect on some of the research done on mycorrhizae and pathogens.
Now, I’m just going to go over a little bit of how the systems work basically. You have the tube in the ground. The imager, you just dig a hole in the ground, install the tubes—you want to allow the roots to grow around them. Once that has happened you can insert the imager into the tube, begin scanning, and then the imager will actually go around at 360 degrees, do a full scan and then you can change the depths with it. Doing that, you’re actually able to get a lot larger picture of the root system you’re looking at. Now, this is going to keep playing so I’m going to go to the next.
That kind of simple application allows a non-destructive testing for a lot of different applications including root turnover, fine root growth, root hair formation, branching patterns and behavior, control versus treatment effects, root distribution, root interactions with like parasites and mycorrhizae and nematodes, and actually a whole lot more. So, you know, we can do a lot of the application studies and tests here on our site, but a lot of this work is actually been done by researchers like you and I’d like to kind of just show some of the examples. We do show some of these on our website.
We try to get as many of them as possible, but so many are coming in where they’re using, especially the 600 since it’s been around for 10 years now and then the 602, even though it’s been around for only a year, there’s already some requests coming in. But these applications are a wide variety. Here you can see they are across the globe from China to Spain to the United States and they’re interested in a whole host of different species and affects, unlikely shrub species, we have a lot of crepe studies as well, wetlands, this is able to be able to be used in—and actually it’s study used in permafrost and the tundra which we’ll see in a little bit. So, being able just to use a fairly simple, you know, idea, being able to scan these roots but at different roots and doing it at a quicker, faster way and a better way of handling the data enables a lot more studies and a lot more work to be done in whatever field you’re looking to do it in.
Now, I’m going to kind of cover the CI-600/602 installation and some of the methods of putting these tubes in the ground, mostly because that’s most of the questions I end up getting right before going to root snap. So, with the CI-600 and 602, we do suggest if at all possible, you install all root tubes during the previous season just to mitigate as much of the detriment to the soil, the detriment to the roots that you’re going to run to. Now, the plant by plant—it’s actually going to be a bit different with your growing season, some plants are very fast and rapid growing, some plants just dealing with a poplar tree root issue and those for trees are very rapid but for most other plants, I wouldn’t call that at all. But the more important this is when you’re installing these root tubes that you just remember that you want to keep the environment as similar as possible in the soil around the tube so that means not allowing UV light in, not allowing moisture in that is atypical to what you would typically find in that area of soil, as well as actually any other temperature and environmental effects. So, when we do sell these tubes individually and when we give you the six ones with the instrument, we actually have insulation caps and give a bit of the ability to buy a gas-powered auger to install these.
Now, the other things I definitely would mention off the bat just having run into this experience myself is, you know, you want to make sure that the soil is not completely compact around the tube. You actually want to keep it about the same density as you would typically find around that plant that way the roots grow as they typically would and not either bunched up because there’s a lot of space and they need a lot of space to grown or completely avoid the tube because you have compact the soil around making it difficult for them to go around the tube. That being said, we have seen the 600s and 602s actually work in an entirely variety of different environments. This includes tundra, this includes wetlands, this includes very rocky soil, as well as very, very sandy or very clay-like soil as well. The set-up can actually also be done to do repeated scans. Now, in this picture you see from the University of Copenhagen, you can tell that they’re inserting the 600 into an already—a tube that been covered in, it looks like duct tape, just to make sure that UV light does not get in for their study, but what you can also do with that if you wanted to do a singular location and just scan over a long amount of time, is you can actually just tell the software just to do repeated scans every five minutes, 15 minutes, up to actually 12 hours. So, if once you put that in the actual scanner will just sit there and every say five minutes, it would make a scan of the roots and again for 12 hours and you can do this as long as it’s plugged into the computer and the computer has power.
So, there are many methods I also want to mention of installation. We do typically suggest using a 45- or 60-degree angle. This is a little bit for historical reasons as well as the—it does keep out, especially in environmental, it helps keep out things like rain and other environmental factors, but this instrument actually works either vertically or horizontally as well. So, you can actually—and I’ll show you a little bit later in the presentation, you can really install it in a lot of very genius different methods. So, and just to give a good example, here we see different tubes in a horizontal method. They have actually installed them right throughout the bed of these different boxes and this is able to—you can take the scanner out and place it in one tube, do your scans, pull it out, place the cap back in, and take the scanner out, as well as—and just keep doing that repeatedly, fairly rapidly. Being able to get a full record in that—especially in that box of all of these root systems for all of the plants right there. In the right just, kind of showing some of its abilities to work regardless of the environment. You can see it there being worked on the tundra. The 600 is doing scans there and we found it’s-- actually the acrylic tubes have more problems with the cold than the instrument itself in using studies.
And then just bringing it back to kind of a success of different studies between like wetlands and very dry temperatures. We have Dr. Maruthi and Dr. Srinivas at the Central Research Institute for Dryland Agriculture in India. Here they’re just studying root growth and development of two maize cultivars under two moisture regimes. You’re looking at actually one moisture regime right now and as you can see they kind of used—they’re covering part of the acrylic pipe with PVC pipe just so, especially in those small biomes, you’re not allowing the UV light in and to keep the roots from growing around the tube.
And here we see more of like and orchard application where we do have the 45 to 60-degree angles of tubes. But again, this actually right around different pumps, right around in very—sometimes very moist, sometimes very dry environments from Damiano Zanotelli of the Free University of Bolzano, Italy. And it’s just to kind of give some of the breath of applications. You can see here that he’s studying roots dormant during winter months, as you can see highlighted using the root snap software. And then, activity and growth in the spring and summer. And being able to do that is just because you’re able to take this instrument and scan in the same location repeatedly and I’ll show a couple of techniques a little bit later on, on how to scan the same spots.
But a lot of the work—so, the scanner itself is really just for scanning and making sure you can do it out in the field. It is connected to a tablet that we do provide, and we’ll show it in a little bit. And the tablet actually will be coming with the software for scanning, calibrations, as well as our RootSnap Image Analysis Software. This isn’t to say that only the tablet can run it, it’s just what we’ve found to be the handiest when you’re out in the field. The image analysis software can actually put on pretty much any computer, as well as, the scanning software.
Now, the great thing with this is actually you can start playing with it today if you would like. We do provide it for free on our website and we also include it with each one of the 600s and 602s and we’re constantly updating it—there’s actually some updates being pushed fairly soon, within the next month by our software engineers. But it is a very easy and fast tool for analysis, prevents backlogs of root images by being a lot quicker way than more traditional ways, and it has a few features that I actually really enjoy, I think they make root analysis a little bit easier than I typically been accustomed to. But then using the roots where you’re actually mapping it out, it actually does automatic calculations, so you can get things like root count, total root length, total root volume, total root area, diameter, length, area, volume, and the average, window depth. You also get the date and time of the images, so you can actually do a very quick study on what times, what variables that you might be running into. You do get actually a physical size of the image. I’m going to show you in a little bit. As well as being able to do scans and as I said before, interlace them together to make a larger picture. And then from that you can actually get things like, not just the individual roots but overall system architecture for like branching angles, branch counts, and diameters of each one of the individuals. So, let’s take a look at what that looks like.
Again, let’s use Dr. Maruthi’s scan because I really like the coloring. And here you can see on the, up here, on the left, these are actually multiple scans put together and stitched together using RootSnap. And so, we will blow up one of these little sections just to see what they’ve done previously with their root scanning software and how it can look when you have mapped it entirely out. Now, as you can see, many individual roots are present in a single image so for each root colored mat, the data that we discussed in previously slides has been recorded automatically in the software and you can actually open that up and view it at your leisure. It does open in up in like a panel side, so you can actually just watch it change as you’re doing your adjustments to your roots.
So that is the bulk of what I was going to discuss with the CI-600 and CI-602. We do have a whole range at CID Bio-Science of different instruments to work with so, including the CI-110 which is a plant canopy imager, which we actually just gave a webinar about a month ago on. And the 202, the 203, both leaf area meters. The 340, a handheld photosynthesis system as well as the assorted software for each one of the devices and a CI-710, which is just a miniature handheld leaf spectrometer. So, all of these are also available. I’m sure at the end of this presentation we’re actually going to be putting out a poll to see which one, you know, you would like another webinar on and we’d be happy to have you vote on it. Now, are—Suzie will be sharing a presentation on the video. Just giving an in-field representation of what it looks like if you’re running this and I’m going to give a little bit of a discussion and kind of explain what’s going on.
So again, we’re seeing images of the CI-600. There you’re seeing the locking nut to keep the serial port in place. Now, really being able to do non-destruction imaging in the field. Here we’re going to show you just all of the pieces that come with the instrument, including the calibration tube. You have the scanner itself, as well as a slider rod—actually there’s like a dozen names for this thing, but what it does is you can just attach it in to the scanner like so, slide it in, slide it out, using the wheels attached to the scanner and those rods actually have different links. So, you can use these links with the cap, which we also provide, to kind of measure out as you’re placing the scanner into the tube and then using it at different depths. And then it’s pretty simple.
This is actually the laptop right now that we are providing with the CI-600 and it’s fairly plug and play. Once you do a calibration, this is a home position. You stick it into the calibration tube and we do suggest that when you’re doing your individual tubes you actually utilize those two dots as well, kind of marking it at each one of the tubes, that way when you’re doing your scans, and you’re placing it in, you’re just getting the exact same scan location every single time. We find that it just makes research and data a lot easier. It’s not a complete detriment if you dont because it is a 360-degree scan. These are some tubes we have actually installed in our own area. We do put kind of a foam core in to keep the UV light but as you’ve seen duct tape, PVC pipe, there’s a lot of different methods to make sure roots are growing in that area. In here we’re actually putting the locking cap on. This locking cap you use to both make sure that different environmental effects, UV and moisture are not getting down into there, and changing the environment, as well as you can actually lock it in place with the slider rod and just change the depth that you’re using it at. And to scan it’s pretty quick. So, here we have the RootSnap software in use. So, you can see on the left I have a certain set of image statistics set up, but you can use it just on your computer very easily using mouse. You can actually change the diameters just using the scroller if you’d like. The image as well just so you can visualize better the roots. I prefer actually using the touch screen variable because it’s—especially when you’re doing a lot of roots very fast, it’s a lot faster method. It does do some thresholding, so you can kind of get an idea of how much roots are in the bulk of it but also, as you’re mapping it out, it’s doing the selective points and taking all that data with it.
So, one of the things, we wanted to thank you all for joining us today because this is—I know this is a bit of a bite of time out of your days and you know, we just wanted to make sure we show our appreciation. We are offering, just by getting a quote today, the two—well actually it’s three extra tubes for free to the additional six. So, that way you’ll be getting nine tubes. If you order the CI-600 through this quote. Now, this is no obligation. This is just receiving a quote, getting an idea of pricing for your region and it’ll be just for that and for attending this webinar you’ll be able to get three tubes free.
Now, to do that, Suzie is actually going to be putting into the chat box the URL that you see ahead of you. So, you’ll be able to go through there and request a quote. I’m going to give you a few moments to do that as well as go through some of the question and answers and we’ll start that next and we have a quite a few popping up, so. I’m really glad to see this many questions coming out and we’ll try to get to as many of them as possible in the time we have. But I’ll give you a few more seconds—actually another minute or so to, you know, make a request if you would like. Just clicking on the URL and I am going to go over some of these questions really quick.
I’m going to sign on in just a second, I just wanted to get a drink. Okay, that was a lot—plenty of time. If not, absolutely no worries. You actually can use that link, now that you have it, pretty much at any time you’d like and just sign on in, we’d be happy to help. And we’re going to go to the questions and answers. So, the first question I have actually shows up, “Are there any improvements on the speed by which digital images can be processed?” This is actually one of the things we hear a lot from students so, that—even with the lower technologies, the lowest DPI would take a long time to acquire data. The 600 has been around for 10 years. When we originally established, you know, we were using a lot older laptops, we’re using older scanner technology. Since the subsequent update, since using laptops that are at faster processing, we’ve actually seen the times increase—oh, decrease considerably. But really, increase in the amount you can do in one area. So, I’ll give an example, if you wanted to do 100 DPI scans, honestly, in the work I’ve seen in the work of other researchers you can get down to just a few seconds to 10 to 15 seconds to do a full scan ahead and then the higher the DPI, definitely the longer the scan is going to take, but, especially with the 602 that has been—the time has been decreased.
The next question—“It’d be nice to know if any development done to the software to get the statistics of the roots, including total length by single click as done in destructive image analysis.” So, there has been some adjustments. I kind of went over a few of them to get the full information from the root system, but we are more than happy to add more. I might have mentioned previously; our software engineers are currently developing another update for the RootSnap software and any ideas or we are definitely happy to entertain as that software is being developed. It’s very important for us that it works as easily for you as we can hopefully get for us, and once that’s done we will send that out to you for free.
The next question I see is, “Does it produce 3D route system architecture?” Right now, no. But that is a very—actually a really good idea for future development. The next question I see is, “How to install it in say a hydroponic setting?” That might be a bit more than I can go into detail here on this slide. The thing I do want to mention is that the instrument is very resilient to different environmental effects with the caveat do not just stick it straight into water. Like most electronics you don’t want to just submerse the whole thing but even if it’s a high moisture, maybe humidity, we’ve had it in 95 plus and it works just fine. Just make sure that you are installing it and you have those installation caps. Make sure that the environment inside is the same as what you want that soil environment to be. It’s going to ambiguous throughout, so that’s maintaining temperature, humidity, UV—well keeping UV light out and we help a lot with our insulation caps as well as some other actual—in our manuals and online materials, some how-to’s to fully do that.
We have another question—“Do you have to install before planting?” I believe it’s asking. And we do definitely suggest installing before planting, however we have had researchers actually installing afterwards. It’s really very much a plant by plant dependent situation. If you think your plant would be resilient to having an auger getting to close to it and a tube installed and it would still grow around within a matter of weeks, that’s going to be fine. If that’s going to do detrimental harm to the plant structure, I would not suggest doing that. So, ironically enough in this case what I usually find is like grasses are a lot harder than things like trees and shrubs.
“Do you have microtubes during certain pots, three centimeters by three point five centimeters in height?” No, we do not. Actually, the shortest tubes we have are one meter. We do actually provide—there are other lengths of tubes, I think you saw, actually, a few of them out there but we definitely want to make sure that the full scan head which is 34 centimeters by six point three five centimeters, is able to be able to do a full rotation. “Is there a special technique to install the tubes and insulate them to avoid moisture? Dew drops inside the tube will supplement the images and give wrong readings.” There are, again, these are very environmentally dependent but the biggest, biggest thing we have found to mitigate that is just making sure that you have both the insulation caps on, if you’re not near the tube and if you’re at the tube doing your scans, just make sure you’re having that locking cap in. That helps mitigate that quite a bit. Also, we’ve found that there is different types of—depending on the environment, say, for example, if you just have a rapid change in temperature in the soil itself, you’re going to see a bit more moisture reflection.
“Can this instrument be used for nematoid analysis?” I actually removed that from the presentation very silly of me and the answer is yes, it actually has been used very frequently for nematoid analysis and especially since the 602 is now able to get down to a 1200 DPI, which is very high resolution, you’re able to really start categorizing a lot of nematoid cysts. “Can you see mycorrhizae with the root images?” Yes. I believe I had one picture on the slide that was showing some of the mycorrhizae’s in root hairs, but yeah, you can definitely get down to that level. Now, with those higher scans I do want to say that you are—it is going to take a little bit longer to do a full scan around, but you’re able to see it. “Is it practical in pots for alfalfa roots?” Very much like the, kind of like small beds I was showing earlier—we actually have tested and had other researchers work these in pots. It just depends on how you put in that acrylic tube. So, if you have the tube go straight through the pot here and have the alfalfa grow around it, that’s one method. You can do it diagonally. Honestly, every time I think that we have run out of ways to do it, I see somebody else come up with a new method.
The next question it looks like, “How many times can one tube be used?” The tube actually can be used for years on length. The most important part is just that that tube doesn’t get scratched up and damaged, so, you’re not really getting a clear viewing of the surrounding root system. Using acrylic, we have found has mitigated a lot of the problems of past—yeah, past different substances, but if you have a ground, like when you’re doing your installation, that’s when you’re going to be getting most of the damage done. Once it’s actually installed and you make sure that there’s not water and that the insulation cap is on, you should be able to use that tube repeatedly pretty much as long as it’s clear. If you do get water into it, and say, like you have standing amount of water, I definitely suggest don’t put the 600 or 602 in there, that will likely damage it—it’s kind of hit and miss and what we do suggest is that you drain out that tube if you’re going to continue using it.
So, the next question we got, “Is a 45- or 60-degree angle, what is the soil depth being monitored?” So, we do handout one-meter tubes however, you can use even longer tube than that. So, you can actually just do a soil depth of, I would say two meters fairly comfortably giving enough sliding rods. After that, you’re starting to get really—it gets kind of difficult to handle it, just as a person. You need more like machinations in place to do that, but you are able to do scans at each one of those depths so, that way you can just—if you want to get a massive picture of what you’re looking at, you can stitch all those scans together. So, the image size taken in one scan actually that’s just depending on the—well, that’s actually a multipart question to be honest. It is measured by just the scanner head of the device itself so as I already mentioned, it is actually just 34.3 centimeters by six point three five centimeters of a scanner head on the 600, but when you stitch all those images together you can get a far bigger picture as well as, when you’re changing the DPI of it, that size of image is going to be the same, but you’re changing the resolution and pixel count. So, it’s—you can get a lot larger data files if you go to a higher resolution.
Ah, here’s another one. “How do you deal with air gaps around the tubes after insulation?” That’s actually, depending on the soil can be either almost a non-issue or an extremely difficult issue. There’s actually a lot of methods online. I would suggest starting with our website and seeing some of the ways it has been applied by other researchers, or even check out like the University of Copenhagen or the Permafrost Institute, they’ve had a lot of issues in dealing with that, or I would be happy to take this online. We are offering consultations on the side and be happy to discuss that. Alright. The next question is, “Did you experiment with this technology with vegetable crops?” So, yes, actually if you saw in India it was being used with maize. The picture I believe it’s still on the screen, it’s being used with corn and corn rows, but it’s also been used with squash, beans, tomatoes, actually, the list is very, very, very long. Since 600 has been in use for over 10 years, it’s a well-documented. 602 has only been around for about less than a year now, but it is fairly similar instrument and it’s getting very similar research.
The next question is actually a very good one. “How often do you have to calibrate?” So, you don’t have to calibrate after each measurement. We do calibrate—request you just stick it in the tube, press calibrate on the screen, and do that either once a day if you’re staying at the same DPI and fairly similar temperatures. If you are changing temperatures like say going from one acrylic tube that is at—I’m from America so, it’s going to be 80 degrees Fahrenheit and then going to another one where it’s say 50 degrees Fahrenheit of the soil, you’re going to see that the acrylic tube itself is actually going to change its diameters just slightly. So, we actually provide a way to adjust the scanner head on the device itself. It’s really simple, just adjust the screw, the scanner head will raise a little bit or lower a little bit depending on its connection with the acrylic tube. We make that really easy but after that you definitely want to calibrate again.
So, I would say keep that white calibration tube with you. To calibrate, it’s really easy. You just stick it in and make sure it’s in the home position and press go. Also, if you’re going to change the resolution—so, say if you want to an initial soil scan, the topsoil, you’re going to do 100 DPI because you just want to get an idea of where the roots are there but the lower you go, you know, that where you’re going to want to see like your mycorrhizae, your finer hairs, your parasites, so, at that level you want to get more to like to 600 and the 1200. To that, you would have to scan at the 100, pull it out, do the calibration at 1200 and then put it back in. Thankfully because you can measure it out, you’ll be able to know where those screens overlap, and you’ll be able to tie them all in very quickly by using RootSnap.
The next question is, “Will the tube influence root growth?” So, acrylic tubes have been long studied and installation and how its installed is the biggest factor for effecting root growth. Making sure that you have the environment and the soil around it, very similar to the roots, that how it was growing on the rest of the plant, is very important and that means make sure the soil’s not compacted, making sure they have the same moisture rate, you’re not having larger amounts of holes in it and you’re also being able to cut out and make sure UV light is not getting into the tube. So, the insulation caps help with the UV light, though I definitely suggest if you’re having large parts of the tube stick out of the ground, make sure those are wrapped up, either by some of the examples have been PVC, duct tape, really or even, you could do white paint, but just some way to keep out the UV light from getting down into the ground and inhibiting the root growth.
The next question is, “How much faster is the 602 compared to the 600 at the same DPI?” And Charles, it’s actually been about twice as fast. We have found that it’s a little slower when it’s cold but it’s about—you’re using a lot faster pace than the older 600s. Actually, the more updated 600s are moving faster but you know as technology increases in one, technology increases in the other. “Can you use RootSnap for root images obtained by other scanning devices?” The answer is, yes, actually you can import really any image into RootSnap. It’s not going—if you import an image that’s not roots you might have some issues simply because it’s trying to delineate between root and soil, a lot by color contrast, light contrast and brightness. So, it’s not going to be—if you’re trying to put your picture in it, it’s going to come out a little funky, but you’ll be able to use it for other pictures.
“What is the recommended DPI for studying root hair mycorrhizae?” 600 to 1200. I’ve seen the CI-600 doesn’t go down to 600 or 900, I would say go, keep around there. For larger colonies, but yeah I would definitely look into using the 1200 DPI just, so you can get the full—as good of resolution as possible in your studies. Let’s see, “How does it work for bigger roots—perennial trees?” Because of the scanner hear it works fairly well. Of course, it really depends on the root size. If you’re thinking about roots larger than say a couple inches, you’re only going to be getting them at a glancing angle to the tube so, it’s—you’ll still be able to see a few but you’re not going to be able to see nearly as many as you would of like the smaller root structures and systems.” Next question is, “What is the technology used in the scan, if it’s divisible light?” Currently, yes, though we are looking into further technologies including different LED pigmentations, different—some light NIR, not too far into the range and also some UV—and seeing how that could be readily added to the scanner. We’re not ready yet, but we are researching it.
The next question is, “Can I have a copy of your PowerPoint slides?” And the answer is yes. Actually, once we actually are finished with this presentation, we’re going to take a recording, I’ll make it available to everybody as well as take the PowerPoint and be able to get it out to anybody who would like to take a look at it. The next question is, “Estimating nodule size and number?” You can kind of do that with RootSnap, that is correct, and you can, just by adjusting say like, which color, which one of those lines and diameters you can get a good size diameter overall mass of your different nodules. So, the next question is, “Is the technology able to detect and identify root disease?” Now, the answer has been yes, it has been able to detect it. It is just the visual scan, so it does require an expert right now to be able to identify, is that a root disease? Is that discoloration from the scan or like the surrounding environment? It still requires the human touch. We are able to pick up root diseases of a very large amount, just simply by being able to scan in areas where you typically couldn’t see.
So, the next question is, “How long can a tube last in the outside environment, especially under freezing conditions?” That’s a good question for acrylics. I know the CI-600, the scanner itself has been used throughout an entire day long of permafrost studies, so I know that will work. With the acrylic tube, I would have to ask some of the experts in the field regarding how those—how long they stand but I do think it’s years. My interest would be decades, but we definitely know it’s over—if you’re looking at two different seasons, you’ll be absolutely fine. The next question, “Is there a special application to suggest the CI-602 to a customer?” We do have a couple different reasons I would suggest the 602. One is that the 602 does go up to 1200 DPI and is a little bit faster scan so you can actually be able to do more rapid scanning with that and at higher resolution. So, if you really need to do, like the parasite studies, mycorrhizae studies, a lot of fine root hairs, you can get it with the 600 at the very edge, if you need to, but with the 602 you can definitely do multiple choices of that resolution level. The other thing I would suggest is because it is a thinner, it does fit—there’s a lot of two-inch diameter tubes out there already from older technologies, and it does fit in those if you have them already established.
Let’s see. The next question is, “Is there a miniature version available?” And currently, sad to say there is not but that’s something we can definitely keep in mind as we continuously progress the advancements of this technology. And next one is, “How sensitive the cameras are to soil types?” Actually, so the camera itself, as long as you’re making sure that scanner head is up against that acrylic tube and the acrylic tube is not deformed or scratched up itself—very, very sensitive and able to pick up your different soil types. You can see each one of the visible scans. So, you can see very rocky, very sandy, very clay, as I typically find where I’m usually from, but you can definitely pick that up pretty readily with the scanner.
Now, using these tubes, since they are acrylic tubes, they are fairly resilient, but the next question is dealing with them deforming below ground and the answer is, anything—there’s very little in the ways of a clear tube that cant deform below ground at this point, if you’re giving it the right conditions. If you’re flooding the ground, if there’s a lot of pressure, but the biggest thing I find is the initial installation that really dictates how well that tube is going to perform as you’re using the scanner on it. Usually after it being installed and after it’s settled, and the roots have grown around it, those tubes are usually pretty much good to go for the long haul, for many years of study.
The next question is, “Can we still have the option when rhizotrons software instead of RootSnap?” And the answer is yes. Actually, the scans are all being saved in a couple different methods, both with the data alongside as well as just a simple image. You can take the image and put it in minirhizotron or any other software you’d like. The next question is, “What does the tip of the tub look like?” I’m going to say like the just toward the screen, we actually have insulation caps on both ends and that’s what it currently—both of them—you see the larger diameter for the 600 and the smaller for the 602. The next question, “Is it possible to measure cassava roots, especially necrotic tissues and cassava roots?” So, personally I know there’s a research already been done using 600 on cassava roots. However, I don’t know if it’s been done for necrotic tissues, I would imagine since it has been done for necrotic tissues of other plant species, unless there is some other variable I’m not aware of, it should be able to be useful for that use.
Alright, the next question is, “Any reason for not being able to save a traced root image for later view or analysis on a computer outside the software?” Actually, that’s a good question. I think one of the most recent updates of this software has been to be able to save those traced images as actual just images, so you see the tracing, simply because I was just able to do that for this slide presentation. But, if you’re asking for like the data associated with it, that would be part of the software since it is a lot more data and needs to be handled differently.
I’m going to answer a couple more questions, however we are getting to about 8:55 my time and wherever that is globally, so we’re getting right into the other part of the hour and we still have a lot of questions coming in. So, what I would like to do is just make sure—just emphasize that, you know, I am available and my compatriots, colleagues are available for a discussion on your individual projects and be happy to consult with you. There is a link that I think Suzie should be adding into the chat fairly shortly that you should definitely check out, click on, and set some time aside so you can talk to myself or Katrina and we would be able to help you with any of your projects, especially when using the 600 and 602. But I will answer a couple more and then we will probably close this out and—okay, we have a lot more questions coming in actually. So, once I answer a couple more I will close this out and end the presentation and we will share this all with you by later today.
Alright, the next one is, “How long does it take to get the total root length of a typical, single-depth 360-degree scan?” Actually, it’s very—oh, if you’re talking about the full scan, you can get it—it really depends on how complicated the root structure is to be honest. If you have a fairly simple root structure, I’ve seen it done within 20 minutes or less. If you have extremely dense and very complicated and you’re mapping out each single one, that is always going to be a longer affair, so I would—but it does do some automation in the software itself, so when you do say a few lines, you’re going to do automate, and it will try to estimate by the pixels, how long those roots really grow. I find that very useful towards the ends, it gets a little wonky, but you just snap it back into place real fast and that makes the process a lot faster. Again, the next question is, “Do we need to calibrate on various DPI?” And, the answer is yes. You want to calibrate before every single—if you’re changing the DPI, you do want to calibrate again, but it’s just a simple as pulling it back out, knowing where you had the depth before just by using the length of the rod, putting it into the calibration tube, scanning, calibrating, and then pulling it out, putting it in for the resolution you’re looking for.
And, the next question is, “Can the software automatically log and save the root readings?” And the answer is yes. It does log them, it does save them. It keeps them in a root scanner file which you can open up later on—I’m sorry RootSnap file that you can open up later on at any time. You also can save the images themselves, so you can open up in other software or just view as you please. The next question, “Can the image analysis software recognize roots?” Traditionally taken in a long time to manually select roots and measure the lengths and images at certain time intervals to get root growth. Again, the image analysis, we have looked at outs of the automatic selection a little bit. So, you’re actually able to start, especially the selection and then just click automate and it will continue on through the similar size pixels. Once the pixels get too different in their coloration, brightness, intensity, it will stop but then you can—and if that is not exactly on your root, you can really quickly just point, drag it over, and it’ll snap back into place.
So, the next question is, again, “How big of an area can be measured?” That is simply the scanner head and dimensions. So, you have 34.3 centimeters of the scanner head. You can scan that and just keep doing that for like six degrees of—I’m sorry six centimeters diameter long all the way through and you could do, I would say, two meters very comfortably and I’ve known some researchers to do more.
And then, the other question actually, and I would say we would finish this off with—we do have another webinar being presented today for this—it’s the same one, but if you were unable to attend this one in time, you can actually sign on to that one. It’s at six p.m. pacific standard time and we will be able to give the same presentation, as well as answer all the questions that you have available there. But, again, my name is Dennis Fischer and we have—if you have any questions following this, please join on to the consulting link that Suzie has provided, and you will be able to set up some time with me at your leisure and we’ll be able to discuss your project or how you would like to use the CI-600 or 602. We can also discuss a lot of other applications and instruments because the CID line is fairly broad. Now I believe Suzie is going to put a poll for what instruments you would like to see on webinar next and then we will wrap up this webinar. So, go ahead and vote what you would like to see more of a presentation on, learn more about and that way we can focus our efforts in the next one coming up, probably within a month or less and be able to get that information out.
Sorry, actually, and also with the voting, you just want to make sure that the URL for requesting quote is also in the chat as well in case you want to do that. And again, I want to say, if you use that particular link, you’ll be able to get the three free tubes for free whenever you or your university or group are able to make an order for the CI-600. This is just for us to make sure you are able to attend the webinar and we want to make sure that we are showing that we are happy you are here, and we give you three free tubes. And again, I would like to thank everybody for coming and look forward to talk to you in future webinars.
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