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RootView User Manual 20 July 2011

1. Sean ID 953 Name Souls 6 Recurring Scan 00 00 1X daily Scan Time 2011 07 18 01 3600 Staring X 100 mm Staring 100 mm Ending X 150mm Ending Ye 600 ra Dx SoL mm Dy 226mm Dwil Time 130 ms Scan Lines Horizontal Sean Mode Shute Step Units mm Star Time 2011 07 18 013608 End Time 2011 07 18 0629 02 Scan Stats Completed Root grows down No Notes User mike Total numberof images 377g 7222 Total Disk Space 289375 Mb Total Travel distance 1159948 mm Estimated Sean Time HE MM SS 0331 58 Scan Time HH MM SS 04 52 54 The left side of the View window displays all of the metadata associated with a given Scan ID A thumbnail composite Mosaic of all images captured during the scan is drawn in the middle of the window At the top are options for how to display selected tiles The default Popup NxN is one tile Selecting other values such as 2x2 or 3x3 will display multiple tiles in a matrix of that many tiles Note that the selected tile will always be in the bottom left corner of the matrix and that if tiles are beyond the edges of the mosaic they will be intentional blank in the matrix or an error message will be given As the mosaic is moused over values are displayed indicating a tile s position on the page X Y as well as the mechanical position of the motors Xnn Ynn The former is especially useful when working with another researcher at a different physical location as
2. Build movies fom prepared Time Series There are three options available for each file under List of Time Series Files Delete is obvious Build a Movie will pop up a window allowing a user to create an AVI movie with a new name and a selectable frame rate Download will start an immediate transfer of a zipped folder of all images in the series to the user s computer ajri Te a ie E Mos Visited B Frefox Help E Firefox Support C Plug in FAQ S Google M Gmail CateCam C Axis GateCam C Google Talk Gad C P6310 gt E Bookmarks D CED C C GD CD CD AMR Soils Node 6 vzs Edit movie parameters for selected Time Series file Build wing Time Series Fle AMR6 Hyphal Growth 0628201 1 07 182011 af Movie Fite Name witout extension ANRE Hhal Geek GEHL STLABODL at Movie Frame Rate 16 mcs por second valid range sO ps In this example we selected Build a Movie from the option next to the Time Series File The resulting screen then presents options for how to build and name it Depending on how much data is in the Time Series File selected it can take from minutes to hours for the movie to be built A good starting value for Movie Frame Rate is 1 frame per second Once Build Movie File is selected List of Pre built movie files will indicate the status of the build Shown in red as processing in the example below oo Root View LA C heeren meron sdu frooriew in
3. Guest account provides a way to position the camera to a given X Y location In addition it provides similar information as Status but also allows viewing of the Motor Log history mostly for debugging purposes and the ability to manually Home the motors Manual motor controller Commands may also be issued but this NOT recommended since they can actually damage to the AMR Manual Commands should only be entered by advanced Users or Administrators The Go To portion of the Motors screen is useful for positioning the camera manually over a given tile It is typically used in conjunction with Show Filename under the SubScan window It is important that the values given in Show Filename are in tenths of millimeters and that the values specified on the Motors page are in full millimeters So a value of 1234 5678 from Show Filename would be entered here as 123 4 and 567 8 in the X and Y boxes of the Motors page Care also need to be taken to verify that the Step Units pull down is set to mm versus steps After values are entered pressing the Go button will send the camera to the selected X Y location Keep in mind that these are absolute coordinates and not incremental If the unit were at 200 200 sending it to 250 250 requires entering 250 250 not 50 50 Also note that any values entered are compared against the minimum and maximum values of the AMR as set by the Administrator e098 Root View Soils Node 6 ra hen Oz so
4. it allows for easy identification of a given tile The latter is useful for finding a given tile based on the filename of the image For historical reasons the origin X 0 Y 0 is at the bottom left of the mosaic This represents the top of the tube so it looks like the roots grow up There is an option allowing images to be captured in the correct orientation but because of the way the filenames are stored those images would not be compatible with older scans If a user wants to begin a new imaging sequence roots grow down could be selected and all of the data collected from that point forward would be compatible When atile image is selected a pop up window is displayed showing the image at full resolution typically 640x480 The image is also highlighted with a small green rectangle in the mosaic Note that tiles will sometimes be out of focus This can be due to the shallow depth of field of the camera the amount of soil compaction in different areas around the tube and the movement of the soil due to insects animals precipitation and root growth L coogeTakcas 0 nesso X cmnseui onp aal ime Di tootmars as Soils 6Recuiag Scan 00 00 1X dally o7 A tile may also be selected using Highlight Tile near the top of the mosaic and entering the X Y value Xnn Ynn Again a useful feature when working with a large mosaic and a colleague at a different physical location Switch to SubScan pr
5. of the filters one must press the Go button at the far right to update the widow Roat View Ae C hno feens jamesreserv edu rocwiew index php ve ie am B Mest visited gt S Frefoxtelp S Freon Support Pog in FAQ SY Coogle Gmail CateCam Arie CateCam Coogle Taik Gad HPGO CENSCW DBp RV gt E bookmarks CEP CED CHP CHD CHP COP CHP COEP AMR6 Soils Node 6 vzs Scan Fiter Seans Sams User Dae Fom Date To From Scan IDTo Scan ID Scans per page Gria AN 2 Ear v z nassen Nene ean Tine avanso Dwellera ma Sean Linas Sean Mede Stat Time Erd Tine Can estad User Sean Situs Are ivedi asss Sow a Raouring Scan C0 Keay 20m areon mm 100 1001000 301228 180 Perumal Sme 201071801388 201107 18082902 O mae Conpeed Merco D ss Sole Rong Som 09 esy zoarroroo mm coosoopososoponezs 180 Horcona mme zottorTotve 9 amamos o mie Comoe ew cone haa ois Rearnng Som 0900 1Xemly Z01 07 460025 mm NODSCODIEOO 0228 180 Horzon Sse 2041071808200 zpINGTABY2028 O min Compe Mew Gone lest Someron San 0000 tKesy 201 07350009 me 1OD CEVNEOADH 01208 180 oreonal Shite a01L07 72n240 apiberAeoLsear O mba Compemd Vow Cony D has sols sRocurng Scar 000 aay zoN1 lt 7 80002 mme TODsCOpEOANHY Go1228 150 Horwonal Snee 201107 140n0023 2DiLeT WOK42 O mie Compie Yew coy o Joi ote rocirng Soar 000 Katy 201147350000 me ciooeoyisoso sonaas 180 Horeonal Shee 01107 190RGNG zDILeTABOLNO O mia Compe Mow Som
6. RootView User Manual 20 July 2011 Based on RV version 2 0 0 18 GETTING STARTED RootView is a web based program for accessing and controlling Automated MiniRhizotrons AMRs It is accessible via a web browser Internet Explorer or Firefox are recommended or in some special situations can be run stand alone on a laptop connected to an AMR in the event a network connection isn t available The primary link for accessing all AMRs is http cens jamesreserve edu rootview Each AMR has three levels of access Administrator User and Guest The Guest account is special in that it is called guest and the password is guest It allows read only access to all data collected The other accounts have varying degrees of write privileges including the ability to schedule new scans and delete old scans Typically each AMR has one administrator and several user accounts The administrator is typically responsible for making sure that the AMR and its associated laptop are running properly and that software on both is up to date There are a wide array of functions and controls available to the Administrator all of which can dramatically change how the AMR functions Further information about these functions is available in the technical manual User accounts are meant for researchers They allow not only access to all data collected by the AMR but also allow the scheduling of scans This manual is intended for Guest and User accounts T
7. as a way to select and generate time series lapse images If a rectangle including a single tile is selected and Create Time Series Data File is pressed a new window is presented offering a starting and ending date and the name of the file to be exported If pressed a button at the bottom of this screen Export Time Series Data to Flipper will then begin searching through both local and archived files for all images contained within the selected area within time period selected Once all of the images have been located RootView returns to the SubScan window This process can take from minutes to hours depending on the size of the area selected and the time period chosen Depending on your browser settings you may be able to observe a message similar to Waiting for cens jamesreserve edu in your browser window In the examples below a tile was selected and the Create Time Series Data file button selected The first window shows the highlighted tile whose highlighted edges can be clicked and dragged to expand or contract the rectangle The second window shows the result of pressing the button along with some editing of fields to better illustrate the example Soils 6 Recurring Scan 00 00 1X daily SubScan Selector Sean m Swenan ton TTo GE Seila Recuring Scan 0920 1x iy p onora oi aao Fon t aa a Suan imam Sare 100 m Tadas X sam Eng oom bx Simm bY 22mm Deel Tine ist me Soins Herat San Mo
8. dex php aale a20 aa Given victed B feton teip S Fraton suppone Plug in FAQ SA Googe Mama camcam aviecaeCam Coogle Talkad O HP E310 gt E teemaks AMR6 Soils Node 6 z Build movies from prepared Timne Series files Note that the reload button on your browser may need to be pressed several times before the build is complete Once the movie is ready the Movie Window will show two options Delete and Download These work in exactly the same way as they do under List of Time Series Files Root View ae D meyen ujoorienjindex phe E A gt cosie Dr Liruginraa 4 coogle Memali cawcam ane GateCam Google Talk Cad C HP 6310 gt E teokmarts LOG OUT Exits the RootView Program and returns your browser to the Log On Screen Additional Information Further information about the design and use of the AMR and RootView software is available by contacting Mike Taggart Sr Development Engineer Center for Conservation Biology Center for Embedded Networked Sensing University of California at Riverside Riverside CA 92521 951 492 9369 mike taggart ucr edu http ccb ucr edu
9. e o Jato Sie cing Semn C0 Xely 2oman s2onon mm HODALOHAEORND 0H 208 tet Hereni Shue 2041 07 12000027 zDiLAT ABOKIE4E O mie Compas ew Oxy D ica SciveReiring Scan 000 ixay 2017 16040 me HODEOHNEOADEY S6r228 150 orzo She zonan oomoa zoa oeeo O mh Meem O Jase Sam Genuin Scan 960 Key 204 0000 mm IAD oopis 361228 150 Herina She 2011079735030 2D1L47 0041860 he Compe Yew omy lasso sole srociring Sam 0000 Keay aomaraoonon mm TODsCOP ISDA Gi2a8 10 Moreonsl smao 201197 e90n000 zortoroooatsoo o mae Compo Mro o hssr Soles Raine Som 700 esy 201107960003 mm oosoopososio ponza 180 Horeon smeo aonomaBooooz zoILGTaROKEK O mia Compe wwo o ure Sais eearnng San 000 Xen mararo mme 1OD JCOHISOMNE 301228 Had Herein Shue a0iva iezsseat zoitarsro4isaa O mh Compie Yew Coe D lsmo Soie8Recirng San 0000 Key ZONIGTCEOKOR mm _ 1ODCOPNEOADH 301 208 150 Horima Shue a01107 080K0882 z0ILeT a8084Rst O mie Compe Mer cw D sses soworaumnosangoco xoay ammarasozos mm pioooopesoeoo 61228 180 Horanaal Sme 2011071502087 20110705002700 O mie Compo yew coy lise Solesroarnng Som 090 mesy zomarosonz mm poosopososio pozas 180 horzomi mme zothorodomi7a7 zoineratokss4 o man Comps vow come l8s0Sois6Roarmng Som 0 1Xemly amarosoz mm ooops onazs 180 orzo Shine 2011070808408 aotaroeisosas O mie Compo Mew Gone Jota Som Rectring San 90 Xesy 201 07220002 mm 1OD 8EHNEOADHY 961228 150 Herina Shade 2011074628492 201L67 a80408a1 he Compe Vow cy D sass sows
10. esents a screen similar to View only with a larger set of features available The intended and most efficient way to use RootView is to schedule full tube scans on a weekly basis and then compare mosaics This allows SubScans to then be run at much higher sampling rates on areas with the most activity Above the mosaic in the SubScan window are two options for scheduling a new scan based on selecting an area within the mosaic One method is to use the Xnn Ynn coordinates from the previous Scan window to fill in the values for X to X and Y to Y The second and most straightforward is to select an area by clicking on a tile and dragging the mouse to select a rectangular area to be scanned followed by clicking the Schedule SubScan button This will bring up a new window similar to the Copy screen that allows for the creation of a new scan Semi s Subscan Area Pom Xi Jio X Nane Soils Recurring Scan 00 00 1X daily Sean Te 2011 07 18 01 36 00 From Y wx Saning X 100 mm Sunne Yi 100mm Ending X 150 Ending Y 600 mm Dx 301 mm Dy 226mm Dwell Tine 130 28 Sean Lines Horizont Sean Mode Shume Siep Unis mm San Time 2011 47 18 01 36 08 End Time 2011 07 180629 02 Sean Status Competed Notes User mike Total number af images 3774 17x222 Tonal Disk Space 289375 Mb Toval Travel distano 11599 83 mm Estimated Sean Time HEMMSS Scan Time i HH MM SS meet vaaia The SubScan window also serves
11. m 600 X NOTTRIPPED Y NOT TRIPPED X TRIPED Y TRIPPED EQUIPMENT PHOTOS The Equipment Photos tab displays photographs of the AMR and is used as an informal way of visually documenting the development process Photos may only be added by the Administrator ABOUT This tab provides details about RootView and the ancillary software installed It is also where contact information and user documentation like this User s Manual are available PANIC STOP This tab not available using the Guest account immediately stops the motors and any scan in progress Its intended purpose is as a failsafe if the User or Administrator observes a motor or camera failure It is possible for the AMR to experience unexpected behavior in the event of a prolonged power failure or if the motor controller parameters have been changed in a way incompatible with normal system function As with the Motors tab it is recommended this function only be used by an experienced User or by the Administrator MOVIES The Movies tab is essentially a repository for time series data collected using the SubScan function Scan SubScan Create Time Series Data file The example below uses the file created earlier in this manual ano Rot View a ja stimode deletetadf 011_012709_057234_013010_057460_20110718 2 v C ajia E most visited mall Caecam Axis Gatecam Google Talk Gad HP E sookmarks v AMR6 Soils Node 6 a
12. ns She Sep ta Sae Tt Jariso13608 Ende Zpltarieocase Sandman Conplind Soe Use mike Toral number of images 3774 171222 Taal Disk Space 289375 Mb The default Starting and Ending dates were modified so that all images at the selected location for that time period were included The default filename was also modified to better reflect the data being collected Lastly Comments were added to add even more meaning to the data Note the bottom of the window indicating RootView is waiting for the cens jamesreserve edu website to respond Root View Jiaj E towimants gt inaa Mcoy Acma O Cancam _ Adiscamcam GoowleTa cad HPesio CENSU AMR6 Soils Node 6 2s Export Time Series Data For Flipper Once the search is finished RootView returns to the SubScan window and new data can be selected When finished the Movies tab can be selected and data can be downloaded or further processed See Movies for further information The final option in this window is Show Selected Filenames Selecting this will return the X Y values in tenths of millimeters of the motor location where the image s was collected as well as the file s physical location on the computer controlling the AMR The X Y values are useful for manually moving the camera toa location independent of a scan and can be accomplished using the Motors tab MOTORS The Motors tab not available from the
13. o logon to an AMR follow the link above Once on the main page there is a pull down that when selected will provide a list of available AMRs If you have a user account you may logon using it otherwise please use the guest account password guest STATUS Depending on if you have logged on as a Guest or User you will see a screen similar to one of the two below Guest screen is on the left User screen is on the right The primary difference are the tabs for Motors and Panic Stop are missing from the Guest screen since they are related to control of the AMR rather than reviewing collected data For the rest of the manual the User screen will be used for examples This first screen is the Status screen and may be returned to at any time by selecting the Status tab at the top of the window It provides a snapshot of the system by listing current conditions In this example the overall system is Idle Other states could include Scanning Homing or Homing Before Scan along with various others The state of the motors and camera are listed separately because they are independently controlled X and Y represent the current position of the motors in this case Home or 0 0 Last Homing Report indicates the amount of error after a Home command has been issued Because a Home is done before each scan this gives all users including the administrator an idea of the health of the motors motor controller and transmissions An er
14. ror of greater than 100 microns on subsequent Homes can indicate a potential failure Fortunately RootView has an alert feature for such exceptions that can alert both Users and Administrators which is covered in the Technical Manual Motor Limit Switches are used when Homing the camera Because stepper motors are used in the AMR it is possible under certain conditions such as an extended power outage for the motor positions to become corrupt By having sensors that can detect when the camera is at the Home position the system can reset itself and continue scanning once the fault condition has been corrected Hard drive free space is listed and monitored by the alert system as well as the approximate number of full tube scans that can be scheduled Even though each AMR has a small dedicated PC to run it and does routine archiving of scans as well as housekeeping of temporary files and archived scans it is possible that an OS update or additional software could be loaded onto the PC By being able to view free disk space a user can be reasonably certain that there is room enough to schedule scans SCAN The Scan tab at the top of the window is used to access completed scheduled running and deleted scans The options for Edit and Copy are not shown when using the Guest account In the example below Filter Scans is being used to select Completed scans by All Users with no date or Scan ID range selected When changing values for any
15. roumnosaneotoixesy aomaroronon me ciooooyesoeoymo2as 180 Horaunal Shee 201L08S02RSeE2 2ONOTOOANEST O mie Compo Yew coe o haso sotesrocuring Soar 0000 Kay 2011 08300000 mme TODsCOpEOANHY Gei208 180 Horeonal Sasa 2011 08 20000025 aoitoesoodtase O mia Cone Mew Sone sta Sie Rcining Som DCO iXey aomaeasonon me HODAEOHAEOADHY oraa t60 Hereon hate ativonaaetes2 aoaea O mk Compin Mew Cony o tansan Compare Mode allows entire scans Mosaics to be compared To do this select the box in the far right column for each scan to be compared then select the Compare button Fit To Screen is recommend in most cases and is the default setting It fits the scans selected to the width of the window you are using in your browser Normal size is most useful for smaller sub scans explained later The example below shows two scans being compared using the Fit To Screen mode To view the length Y direction of the scan simply scroll down ano oot View AMRE Soils Node 6 2001 Compare Selected Mosaics View brings up a new window displaying a mosaic of all images associated with the Scan ID at the far left Copy takes all of the metadata from the associated Scan ID and presents a completed template on a new screen for creating a new scan New Scan below Filter Scans on the left does essentially the same thing only presents a blank template If View is selected a new window similar to the following is presented Root View

RootView User Manual 20 July 2011

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