LabSmith SVM340 Synchronized Video Microscope User Manual
Contents
1. eeeeeeeeeee 44 7 1 1 SEP ex poc n p Ma kA MORD LA tear ae 44 TL2 Creating a PIV probe mi aa 44 7 1 3 Velocity Probe Properties bee 45 7 2 Intensity Dr DGS aoienseaxcnisenssc nn ci kevkac uae Ya cria aerei ni 48 7 2 1 Creating intensity probes w wwwwmmmmmmmmanm amewa 49 1 2 2 Intensity Probe Properties eeeeeee 49 7 3 Recording probe data 50 74 Saving probes ieeusiseseiceecccesessis aca sic ce cun wauza 52 8 TROUBLESHOOTING 52 8 1 Getting help 5 eco eiinrce censeri do ans ainia 52 8 2 INO VIGEO SIQNAl ecc ccconiitaiveadio coxa atssaiv sas as dradEe nic sabi sanus 53 8 3 Video quality iciacetii ctn dion deir Loi Fx Ld Ri Cua Fd 54 8 4 Dropped frames eeeeeeeeeeeee 54 9 SPECIFICATIONS eene 56 1 INTRODUCTION The SVM340 is an inverted fluorescence microscope with built in video camera fluorescence filter pulsed Light Emitting Diode LED illuminator motorized x y traverse and focusing actuator It can directly image fluorescent or non fluorescent samples on a standard video monitor or video recorder In addition the SVM340 includes an advanced programmable synchronization unit with four inputs and three outputs for synchronizing image acquisition to external events The basic functions can be controlled by the fr2. 1 bottle Lubricate focus motor screws bushings located under Delrin stage annually or as needed Standoffs and washers SVM is shipped with the standoffs feet uninstalled to reduce the chance of damage during shipping Install the standoffs in the threaded holes on the bottom of the SVM Four rubber washers are included and can be put between the standoff and chassis to help level the SVM The SVM chassis uses a sheet metal design to minimize weight and cost The chassis can warp slightly during assembly or shipping The kinematic design of the focus stage ensures that the slight warping will not affect the function of the SVM Filters and foam washers As ordered Schott glass filters are shipped with a foam washer The filter is installed on the optics module by removing the objective and placing the filter in the recessed area in the objective mount The foam washer is used to hold the filter in place when the objective is reinstalled Note Take care not to introduce dust into the optics module when the objective is removed If the objective will be left off the optics module place something over the objective mount i e a piece of tape to prevent dust from entering the module 57
3. traverse movements front panel lamps and buttons and back panels inputs and outputs The firmware is included in the uScope application package and can be loaded into the SVM340 from within the uScope software To upgrade firmware to the latest version 1 Download the newest version of uScope from www labsmith com and install on your computer following the installation procedure described in the introduction 2 Connect and turn on the SVM340 and start up the uScope application on the PC 3 In online mode choose SVM gt Update Firmware gt Update All 25 Update firmware gt Update all top mot Update main Magnification Update front panel 4 Click OK when the update dialog box appears 5 Wait while the firmware is updated You can follow the progress in the status bar at the bottom of the uScope main window 6 When the progress indicator reaches 100 the upgrade is completed Important Do not turn off or disconnect the SVM340 or the PC while the upgrade is in progress This may result in loss of communication with the instrument that requires LabSmith assistance to resolve 5 RUNNING uSCOPE SOFTWARE When you run the uScope application it will automatically connect to the SVM340 if it is present on a serial port and turned on If uScope does not find a SVM340 the communications settings box will appear as shown above Select the correct serial port and press OK The uScope main window
4. Adjust typically channel C e Illuminator Max off Adjust adjust adjust Adjust colored lights e EPI light n a max n a n a n a n a channel D EPI e External Room Off off off on light 55 9 SPECIFICATIONS Traverse Range Resolution Sample stage Dimensions Opening Camera module RS 170 BW RS 170 C Objectives Illuminator modules Inputs Outputs Communication interface Physical Dimensions Weight Power 56 x 50mm y 75 mm focus 8mm x and y 10 um focus z 1 um X x Y 140mm x 200mm 55 x 80 mm Analog interlaced monochrome camera with 1 3 CCD 640 x 480 pixels 30 frames s Bayer pattern analog color camera with 1 3 CCD 640 x 480 pixels 30 frames s 10x plan 0 25 170 4x 20x LED B 3 blue center 460 nm bandwidth 50 nm one white bank LED G 3 green center 560 nm bandwidth 50 nm one white bank LED R 3 red center 660 nm bandwidth 50 nm one white LED W 4 white banks LED RGBW red 1 green blue 1 white bank 4 programmable digital inputs TTL level Composite analog video out S video out 3 programmable digital outputs TTL level 4 external illuminator trigger drivers TTL level Serial RS232 9 pin D sub connector W x L x H 208 x 267 x 85 mm 2 8 kg 90 240 VAC 47 63 Hz 100 VA Eguipment List Item Oty Use Purpose 2 washer 1 Objective spacer when trying to view items above the focal range of the SVM Lubricant
5. a polished stainless steel plate which can be machined to provide application specific mounts for the fluidic device electrodes fluid hoses or other fittings 17 SVM340 iesin wn s AT RU p m uU Removing the microscope stage 7 00 x 9 00 rectangle to place the instrument on a plane table surface The feet can be replaced by leveling feet which allow fine adjustment of the instrument or standard optical posts which can be clamped firmly to an optical table Contact LabSmith for more information 2 10 Motion limits To restrict the motion limits on the XY stage select SVM gt Motion Limits Modification of these limits may be useful if you have installed a device on the SVM i e a chipholder that may interfere with the stage at its preset limits 3 VIDEO AND ILLUMINATION TIMING The master clock for the SVM340 is provided by the video signal timing The CCD camera outputs video in standard RS170 format NTSC in the color version which is an analog interlaced format compatible with standard analog video monitors or video recorders 18 Frame 33 ms full frame Fields Even Odd Even Odd Mos clin lim soli sa i mi LED drive lx aata E LED on variable Timing sequence of the illumination in relation to the video signal The RS170 interlaced video signal is composed of two fields called even and odd fields each containing every second line of the
6. analog voltage into 256 different gray scale levels Normally you would use a grayscale LUT mapping the 256 gray scale levels into 256 different shades of gray but you can apply color LUT s for false color display The reason for using false color display is that it is difficult to distinguish 256 different gray levels on a standard computer monitor Converting shades of gray into colors can significantly enhance visibility of small differences in gray scale value You can experiment with false color display by Click Video gt Color format gt Spectrum LUT etc If you have a color camera and you want to keep the color click Video gt Color format gt 24 bit RGB You may also select a monochrome 8 bit with a color camera to save RAM and disk space Color video data takes up 8 bits each for the red blue and green colors and thus consumes three times as much disk space and processing time as 8 bit per pixel video 6 VIDEO RECORDING One of the main features of the uScope application is the ability to record long unbroken video sequences without compression These video sequences are stored in standard AVI format so that they can later be viewed by Windows Media Player or other video playback software off line processed by uScope or other video processing software compatible with the AVI standard To enable uncompressed video recording uScope makes use of a double buffering system described below The buffering scheme also enables pre tr
7. image The interlaced format was defined in the early days of television to avoid flickering TV images The even field contains lines 0 2 4 524 and the odd field lines 1 2 525 The field frequency is 60 Hz with one even and one odd field adding up to a full video frame each 33 3 ms corresponding to 30 Hz frame frequency To ensure that all lines of the video signal are equally illuminated the LED s flash twice during an image once in every field The LED pulse starts in the frame blanking period and its width can be varied from 0 to near 10046 of a field period 16 6 ms Due to the interlaced readout of the camera sensor images of fast moving objects which move a noticeable distance during the 16 6 ms between two consecutive fields may appear jagged at the horizontal edges See section below for a discussion of the implications and tools to control the interlacing effect 4 uSCOPE SOFTWARE The uScope software lets you set the functions of the SV340 and control the video acquisition and on line processing It also allows you to recall 19 and process stored video files uScope runs on any PC with Microsoft Windows XP operating system or later Note The uScope application makes extensive use of the DirectX software which is provided by Microsoft Corp and installed independently of uScope If you have installed a local language version of Windows XP DirectX will install in the same language Consequently some o
8. of 60 Hz This means that every second line of a full image is recorded at a time 16 6 ms later than the other half of the lines As a consequence fast moving objects will be recorded with a slight horizontal blur which is caused by the image segment in the even lines being shifted slightly from the image segment in the odd lines 38 Image of a horizontally moving particle recorded with the SVM340 interlace camera Zooming in on such a fast moving particle reveals the jagged edges caused by the interlace camera format To reduce the effects of the interlacing uScope includes deinterlace filters which will reduce the visual appearance of the blurring caused by the interlacing by various algorithms The delinterlace method is selected in the Video gt Deinterlace Video options dialog box 39 _Live Video Deinterlacing video einteriac Deinterlacing algorithm 9 Do not deinterlace 0 Two frame Bob Blended clipping D Weave Field Bob If vou experience horizontal combs in moving parts of your images your video file or source is interlaced Select a deinterlacer to mitigate this artifact If your video is not interlaced select Do not deinterlace Odd field is first recommended An interlaced frame consists of alternating horizontal stripes of video taken at half the frame period apart Most cameras including those of the SVM present the earlier image in the odd lines field Live Video Dein
9. pulsed illumination image acquisition and external devices in response to up to four trigger input signals In each of these modes you can use microscope objectives with magnification from 4X to 20X and acquire and store the video output on standard analog video storage hardware With the uScope application you can directly store the video data on computer disk as avil files and perform advanced real time video processing 1 4 Computer requirements The SVM340 can be used with any computer equipped with a RS232 port or USB1 0 or greater port and a free PCI slot or USB2 0 or greater port for the video input card However since the uScope software is designed to stream digitized video sequences directly to disk it is recommended that the computer fulfills the following minimum requirements Windows XP Vista or Windows 7 or newer One free PCI slot for the video capture card or a free USB2 0 port minimum of 1 GB of RAM 4 8 GB recommended 80 GB hard disk with 12 ms access time 500 1000 GB recommended The SVM340 microscope includes a VGA resolution analog CCD camera which outputs a standard RS170 monochrome or NTSC color composite video signal The video signal is digitized by a DirectX9 0 compliant PCI video capture card or USB2 0 video capture peripheral capable of digitizing and storing uncompressed VGA resolution video on disk Many PC video input devices include on board image compression hardware converting the video stream
10. to adjust the focus while the and buttons to the left of the bar are used for fine adjustment 22 The focus can also be adjusted using the Page Up and Page Down keys on the keyboard Illuminator As described in the Video and Illumination Timing Section above LED illuminator channels strobe during each image frame The Illuminator control is used to adjust the strobe duration of each channel effectively altering the LED intensity When a standard B amp W or Color optics module is installed the control panel slider bars at the top are used to adjust each LED channel A D as shown below Illuminator Checking the Gang box will cause all LED banks to be adjusted simultaneously when one slider is activated When an EPI optics module is installed the illuminator control will be as shown below Illuminator Gang amp B f c Lit Epi f For this case the channel B slider bar adjusts both the B and D channel LEDs Note The Illuminator scroll bars do not update when the illumination is changed via the SVM front panel If the front panel will be used for illuminator control we recommend first setting all illuminator slider bars to the maximum setting to allow the full range of illuminator control 23 The illumination can also be adjusted to a specific level using the menu SVM LED Settings The following dialog box will appear LED Pulse Durations dialog box The maximum illumination setting is 16600
11. us Presets The presets panel allow saving and restoring up to ten traverse x y and focus positions and illumination settings in storage cells A J Clicking a button will load the stored preset and adjust traverse position and LED illumination to the stored values Checking the Save box first will store the current setting in the selected storage cell Sites A D can also be saved and accessed from the SVM front panel Presets n oa Oy Click the Stop Motion button to stop the traverse 24 For a description of the Video recording and probe functions see sections 6 and 7 below 4 1 usc files The uScope software saves the instrument and video settings in a file with usc extension To open a uScope file choose File gt Open then locate the file on your hard drive You can also choose from recently opened files at the bottom of the File menu 4 2 Online and offline operation uScope can work in both online and off line mode When on line it communicates with a SVM340 controls its functions and accepts live video signals from a DirectX compliant video capture card When off line uScope can open a stored video file for playback and further processing uScope will go into off line mode whenever it fails to locate a SVM340 on the selected serial port 4 3 Upgrading firmware The firmware is the software stored inside the SVM340 in non volatile memory and controls the internal functions of the instrument such as
12. video drivers or video settings o Optics Module issues Is the camera correctly installed in the SVM top of camera box is securely against magnets on bottom of stage Check connector pins on top of camera to ensure none of the pins are bent or broken o Video card driver Select Video Video Capture Device to select the proper video capture device If your video capture device is not listed o If you have installed an internal card have you installed the drivers o If you have an external capture device Is the device plugged into a USB port Is the correct driver installed Depending on your operating system you may need to download the driver from the device manufacturer s website e Once you have chosen your video capture device go to Video Physical Input Connector and choose Video S Video In for the input connector 53 Ensure the S Video cable is properly plugged into the back of the SVM and the video capture device or card e Check the pins on both ends of the S Video cable to make sure none are broken or bent 8 3 Video quality Fluorescence images block room light Fast moving flows use deinterlacing to eliminate lines across screen Steady image use time averaging to improve signal to noise 8 4 Dropped frames The SVM uScope software uses a buffer as it is recording to minimize dropped frames However if the available RAM isn t sufficient you may still experience dropped frames Improvin
13. 4 RS232 Serial CONMECIOP s iieri cis tede are seed aa etus 17 2 9 Microscope stage eese H 2 10 Motion limits Kawa Kawa Kawa Kana wawa Kaka Kaa 3 VIDEO AND ILLUMINATION TIMING 18 4 uSCOPE SOFTWARE 19 4 1 WSC ASS Lruosenixiissei xcci s ud bavs barn cota Qe ri a Coda DEO DA waa 25 4 2 Online and offline operation 25 4 3 Upgrading firmware eee 25 5 RUNNING uSCOPE SOFTWARE 26 5 1 Video options set up eeeeeeeeeeeeeeeeeeennee 27 5 2 Color format set up eee 29 6 VIDEO RECORDING 30 6 1 Video compression eeeeeeeeeeeeeee 31 6 2 Recording Speed riri retirar neri sand seria naria nerd no 32 6 3 BU ASHIKE Eu Lex TEE 32 6 4 Pre and post trigger recording 33 6 5 Recording video insons 00220 seid dass 34 6 6 Snap shols oinnes atsara inie ais aas EKA siasa 35 6 7 DEIMMGFIACING uus cien russia ite ccs cin inde ae a cec Did s xed rus ca CUr 38 6 8 ime lA PS iiio c dta utet cte a CO nea eds uta x CIN akazi 41 6 9 Distance indicator eceeeeeeeuuee 42 7 PROBES sah i mir otelodedratodac c 43 7 1 X Velocity PIV probes
14. ING 8 1 Getting help This guide is your main source for information on operating the SVM340 and the uScope software The guide is also available on the uScope CD in PDF format for viewing with Adobe Acrobat Check the LabSmith web site www labsmith com for user manual updates application notes and information to help you use the SVM340 If you are unable to find the help you need call the LabSmith technical support at 925 292 5161 or send an e mail to info absmith com If you need support please write down the serial number of your SVM340 located on the bottom of the unit and the version of the software you are using To get the software version number click Help About uScope in the uScope main window 52 8 2 No video signal If the optics module is not focused on an object it sometimes appears that the you are not getting a signal This is especially true with the EPI module or a standard module when a filter is installed The easiest way to see if you are in fact getting a signal is to turn on and off the SVM or unplug replug the s video cable If you see a flash or any change to the image you are getting a signal If you are not getting a signal try the troubling shooting guide below e Ifyou have multiple optics modules try another one If only one optics module is not working the problem is most likely with the optics module If none of the optics modules are working the problem is most likely with the video card
15. TN zA 2 New intensity p Repeat step 2 to create as many probes as desired Once created the probes can be moved by clicking and holding the mouse button over the probe and dragging it to the desired location The shape of the probe can also be modified by dragging the polygon points to create the desired shape 7 2 2 Intensity Probe Properties Intensity probe data displayed and recorded can be selected by selecting the probe left click then right click and select Properties The following dialog box will appear 49 Display options Red Green Blue Gray Average Spatial RMS Saturation Maximum Minimum Cancel Triggering Polygon Probe Properties dialog box For images from the B amp W or EPI optics module only the Gray displays are applicable 7 3 Recording probe data Data can be recorded simultaneously from all probes To record data 1 Choose File gt Measurement File Naming to select how the recorded data will be saved 50 Type of file Tab delineated text spreadsheet files dat Y Do not auto name prompt for name Qj Auto name files File path and name root C Users Eric Cummings Documents uS cor Append the date YY MM DD Append the time HH MM S5 4 Append counter starting at 1 Example C Users Eric Cummings Documents uScope 4SVMO00001_1 dat Na
16. below will appear 26 f Ikke navngivet uScope File Edit View SVM Video Help De Soe sez Aj ej cjo sr lt a Rese p Jl Stop Je wama Unlimited ro s Save buffer now Ready For off line mode open the AVI file you want to process off line The SVM340 does not have to be connected For on line LIVE mode click cancel in the Open dialog box for on line operation and click Video gt Process live video 5 1 Video options set up If the video capture hardware dialog doesn t pop up it should the first time click View gt Video options gt Input device 27 e LIVE File Edit RYE SvM Video Help a s NIIINEENEI see Communications options gt Analog settings LEDs Audio options gt Video frame Format Text options gt Input connector B Input device Deinterlace live video Deinterlace offline video Deinterlace options Gang E v Toolbar v Status bar Video options menu video capture hardware Hauppauge WinT Capture Click on the video capture card that you want to use Select the appropriate capture source Make sure that either the BNC composite or S Video connector output of the SVM340 is connected to an input of the Hauppauge card and select the relevant input connector through the Input connector box Click View Video options gt Input connector and select the input that you want e
17. bes should typically be the same size in both x and y directions b Smaller probes require less processing power so use smaller window sizes to run more probes simultaneously c Increasing the probe size will improve the signal to noise ratio decreasing the size will increase spatial resolution d Ifthe probe is located in a region of fast flow the probe size must be large enough that the correlation does not fall beyond the window The Cross Correlation field see below can be an aid in setting the size 46 Note If you cannot achieve sufficient signal to noise ratio with a required probe size you may need to adjust the illumination particle feed etc If the probe is in an area of steady flow then increasing time averaging may also help 3 The Averaging percent per frame values help separate the useful flow information from the background data by weighing the previous frames of data versus the current frame The default values of 9596 are acceptable for most flows Some guidelines for setting the percentages are a The Background mean percentage determines how much of the image field is considered background based on its steady presence over multiple frames Increasing this value increases the amount of information that is ignored such as stuck particles Check the Subtract Mean box see below to apply this calculation and remove the data Decreasing the Correlation value improves time resolution increasing the
18. customized illuminator modules with any combination of LED channels The illuminator module can be removed from the traverse from the top by pulling the module upwards Removing the illumination module Note When reinserting the illuminator module take care that the connector pins are all correctly inserted in the receptacle without bending or damaging the pins Also take care not to apply excessive force Support the camera module from below with your hand when inserting the illumination module and press from below to ensure the traverse mechanism is magnetically seated 2 3 Optics module The optics module is attached to the traverse by magnetic holders and can be removed by tilting the SVM340 on its side and gently pulling the camera module down from below the SVM340 body until it comes free Important Before removing or inserting a optics module turn off the SVM340 using the power button at the left of the front panel Optics module Note When removing or inserting the optics module take care not to apply excessive force since this may damage the traverse mechanism and compromise traverse accuracy 10 2 4 Microscope objective The microscope objective is a standard DIN type objective with 160 mm conjugate image distance To replace the objective remove the camera module and unscrew the objective The SVM340 supports objectives with magnifications from 4x to 20x Objectives with highe
19. d of view the user can set uScope to start recording from a number of seconds before the record button is pressed and then wait to start recording until the event has been observed The duration of the buffered video sequence depends on the amount RAM set aside for the buffer The more RAM installed in the computer the 32 more buffer space can be set aside without slowing down other tasks The initial buffer size is set to half the available RAM but you may want to adjust the buffer size get longer pre trigger video sequence duration Buffer size is specified in The View Video Buffering settings menu RAM buffer Percentage of available RAM Buffer size 534 MB 760 s Video Buffer Settings dialog box Note Choosing the 24 bit option for recording video Video gt Color Format gt 24 bit RGB true color requires 3 times the buffer RAM of all other video options 6 4 Pre and post trigger recording The figure below illustrates the effect of the buffer size on the pre and post trigger recording durations Trigger Stored video Time RAM Buffer Stored video Disk Buffer Pre trigger top and post trigger bottom recording 33 For pre trigger recording you save the video sequence occurring before the trigger stored in the RAM buffer With post trigger recording you save the video sequence occurring immediately after the trigger and temporarily stored in the disk buffer The disk buffer is normal
20. ents have been made to the interface for recording pre and post trigger video Distance indicator The Distance Indicator allows you to measure features on your image 1 2 Package contents The SVM340 package should include the following items e SVM340 microscope main body e Camera module with one microscope objective according to your order e Hauppauge WinTV PCI video input card and driver disk Power cable One RS232 serial cable and one S video cable Installation disk with uScope software This manual Extra objectives illumination or camera modules as ordered If any parts are missing or damaged please contact your local dealer or LabSmith immediately 1 3 Basic functions The SVM340 combines an inverted fluorescence video microscope with a programmable synchronizer and software for on line image acquisition processing and storage You can use the instrument in several ways e Asastand alone video microscope Connect the video output from the SVM340 to an analog video monitor or VCR through the BNC or the S video outputs on the rear panel You can now focus traverse and adjust illumination intensity by the controls on the front panel while observing the image on the monitor e Asa software controlled video microscope for automatic or manual acquisition of video sequences using the on line image processing and storage capabilities of the uScope application e As an integrated part of a complex experiment synchronizing
21. f the dialog boxes shown below may appear in the language of your windows installation The uScope main window is divided into the following sections e The video display window e The LED control panel e The focus control panel e The presets panel e The video recording panel e Probe controls 20 Probe DER controls Presets Csee aj ej cj o stor Presets panel Traverse control Video display window Video md Video duration recor din g C TA cz peii usc le iS oce db bataille al M Ga LUCA En Save buffer now C qf RN i panel uScope main window The video display window shows the off line or on line live video as selected in the Video menu X Y Traverse The position indicators to the right and below the video display indicate the position of the x y traverse and can be used to move the traverse 21 The traverse can also be adjusted using the keyboard arrow keys Holding down the shift key while using the arrow keys slows the traverse to allow fine adjustment The X Y traverse has a motion range of 50 mm by 75 mm This range can be limited by selecting SVM gt Motion Limits and adjusting the slider bars The Motion Limits dialog box is shown below Drag the slider bars to select a new range of motion limits Allowed motion range Back Motion Limits dialog box Focus The focus indicator slider bar is located at the top of the main window The slider bar can be used
22. g Input 0 Video SVideo In Output 0 Video Decoder Out Click OK At this point you should see live video on your screen 28 Properties Crossbar Input Dutput D Video SVideo In Jo Video Decoder Qut X Current Input D Video SVideo In Related Pin Related Pin B Audio Line In 1 Audio Decoder Out Link Related Streams Cancel Input connector selection box You do not have to worry about the audio options since they are not currently used for the uScope application To set the video frame size you can click Video Video options Video frame format Select 320x240 for low resolution images and 640x480 for full resolution images Do not change the color space whatever comes up normally RGB24 is correct Note The DirectX video controls dialog boxes are of general nature and allow settings incompatible with the SVM340 Do not change the Video Standard NTSC M or the output aspect ratio the size must be 640x480 320x240 160x120 or 80x60 5 2 Color format set up The SVM340 can be fitted with either a grayscale B amp W or color camera and the video output should be displayed and stored in corresponding monochrome or color formats This is done by means of Look Up Tables 29 LUT s which convert the analog voltage outputs of the video signal to the appropriate gray scale or color values If you have a B amp W camera you want to make sure you are using an 8 bit LUT converting the
23. g available RAM Set the RAM buffer should be gt 500 MB View Video Buffer Settings Close anything running in the background that might be a resource hog i e Windows Indexer Antivirus scan fetching and scanning emails automated backup etc If you are using uScope Probes close any that aren t necessary Try running without interlacing and or compression Color Format Running in true color Video gt Color Format gt 24 bit RGB uses 3X more RAM compared to the B amp W video options If true color is not necessary chose another option Videos saved in true color will also be 3X the size of B amp W videos The following table provides additional troubleshooting options 54 Video and Image Ouality Module indicates B amp W EPI Color B amp W B amp W Color optimal module for application Color Format B amp W or B amp W or 24 bit RGB B amp W or B amp W or 24 bit RGB Fluor Fluor Fluor Fluor Analog Settings Video gt Brightness Contrast Hue etc Brightness Adjust Adjust Adjust Adjust Adjust Adjust typically typically typically typically low low low low e Contrast Adjust Adjust Adjust Adjust Adjust Adjust typically typically typically typically high high high high e Hue No effect No effect Adjust No effect No effect Adjust e Saturation Min Min Max Min Min Max e Sharpness min min Adjust min min adjust Illuminator Settings e White light Off Off Adjust adjust adjust
24. ic compressor settings should be directed to the compressor distributor 6 2 Recording speed A standard monochrome RS 170 video signal converts into a digital data rate of 8 9 MBytes s which can easily be read into PC RAM memory in real time It is also within the capability of modern fast computers to write to hard disk in real time at this data rate provided the computer is not overloaded by simultaneously executing other disk or CPU intensive tasks Color NTSC video signals convert into a data rate of 26 4 MBytes s which can readily be written to RAM memory in real time but may be too high to write to hard disk in real time In that case some frames scattered throughout the video sequence are lost resulting in a stored video sequence with time intervals of 33 3 ms between most images but with 66 6 ms 99 9 ms or some other multiple of the base frame interval between some individual images Such lost frames are called dropped frames Video sequences with dropped frames are not suitable for accurate time history analysis since it is difficult to know afterwards exactly where frames are missing 6 3 Buffering The SVM s uScope software uses buffering to capture images without dropping frames uScope stores digitized video date in a cyclic RAM buffer simultaneous with the display Buffering also allows the user to selectively record events after they occur For instance to catch a particular particle or droplet passing through the fiel
25. igger recording enabling you to store a video of what happened before the trigger instant 30 6 1 Video compression uScope can use video compressors that are installed on your computer but does not have any built in compression To add compression functionality you need to download and install a codec A compatible codec will also need to be installed on anything that plays the video All codecs are not equal Some compress well Some compress fast Avoid over compressing the data The compression occurs when the video is being captured so it cannot be undone if the results are not desirable If you plan to perform PIV on your data we recommend using a lossless compression The best quality video compression takes time It is often best to save videos with minimal or lossless compression and later post process them Video compression codecs we recommend include Xvid www xvid org Excellent open source compressor Lagarith http lags leetcode net codec html High performance lossless compressor Virtual dub www virtualdub org Excellent video post processor and editor To save a video with compression select Video Use Video Compression and the following dialog box will pop up List of Installed Compressors dialog box 3l Select the desired compressor from the drop down box The options listed in the configure dialog box will depend on the installed compressor Questions regarding specif
26. into various compressed video formats Image compression standards like MPEG are designed for general visual imagery and may not be suitable for all types of imagery occurring in microfluidics device diagnostics e g the images of isolated small particles as recorded in Particle Image Velocimetry PIV experiments The ability to record uncompressed video is therefore an important feature of the hardware and software included with the SVM340 Uncompressed video streams naturally take up more bandwidth and use more computer processing power for display and storage so a powerful computer is recommended When used on a newer standard PC with moderately fast CPU and disk speed uncompressed video sequences can usually be stored on disk in real time If used on slower computers frames may be lost during recording Slower computers may also exhibit a perceptible delay between an imaged event and its appearance on the computer display Also a large hard disk is recommended for storage of video data A color video signal will typically generate 1 6 GB per minute and thus quickly consume hard disk space 1 5 Installing the software 1 5 1 Installing the video capture card and or drivers A video capture card or peripheral USB capture device is required to view and record the video signal on your computer If you purchased one of the devices through LabSmith a separate instruction manual with the installation instructions and driver disk will be i
27. ly larger than the RAM buffer 6 5 Recording a video To record a video set the time in the Record from box to the desired number of seconds or drag the slider bar between now and the maximum buffer size This will set the time duration that is recorded from the pre trigger buffer oO oO Record from Sean no F9 duration 1s 1000s a e Unlimited s LI VI Time lapse Then either set the For Duration time or leave it as Unlimited The duration time represent the total video duration pre trigger buffer 4 post trigger record time If Unlimited video duration is used the video will record until the record button is pressed again The total duration of the video will be the buffer time plus the newly recorded time the time the video button is depressed Note uScope software now uses vido buffering for the video recorded live not from the pre trigger buffer so that this video is also saved without dropping frames 34 6 6 Snap shots A snap shot is a single image consisting of an average of one or more consecutive images Snap shots are taking by pressing the or i button both located in the lower left hand corner of the main window Takes a snap shot using the predetermined frame averaging and other options specified in the Snap Shot Settings see below Ea Takes a snap shot and frame averages until the button is pressed again All other options specified in the Snap Shot Settings other tha
28. ming settings for new measurements dialog box a If you choose Do not auto name uScope will prompt you for a file name and location for each new recording b Choose Auto name files to automatically name each recording Check Append the date Append the time and or Append counter to add these values to the new file names An example of how the name will appear is shown at the bottom of the dialog box Note You can currently only save the probes in the tab delineated text spreadsheet file format 2 To begin recording choose File gt Record or click the Start Stop B toolbar button If Autonaming is selected recording will begin immediately Otherwise recording will begin after you name the file and click OK 3 To end recording choose File Record or click the Start Stop 51 button again The PIV output file will include four columns for each probe the X and Y locations of its centroid measured from the upper left of the window and the X and Y velocity at each point in time The X Y location columns will only have entries in the first row 7 4 Saving probes A set of probes can be saved to disk and recalled later 1 Arrange the probes and set their Properties 2 Choose File gt Save Probes As to create a new probe file Probe files are saved in the uScope file formate usc 3 Select the name and location for the file and click Save To recall a stored set of probes choose File gt Open 8 TROUBLESHOOT
29. n Number of frames to average are maintained Snap Shot Settings The dialog box is opened from View gt Snap Shot Settings 35 Number of frames to average Black level adjust 2 None Auto Manual White level adjust i None Auto Manual Flash Settings None Strobe illuminator Settings Frames to delay before averaging 0 Cancel File naming Snap Shot Settings dialog bor Number of frames to average This is the number of consecutive frames averaged to form a single snap shot If you have motion and are trying to capture particle images this number is typically 1 no averaging However if you have a little to no motion increasing the number of frames will improve your signal to noise ratio for static images the signal to noise ratio will improve by approximately the square root of the number of frames averaged Black and White level adjust Typically not changed Use these values to change limits of the video spectrum In the full color spectrum 0 represents black and 255 represents white If this range is reduced everything below the set black level will appear black and everything above the set white level will appear white Flash Settings None Illuminator will not change when snapshot is taken Strobe illuminator Illuminator settings will change when snapshot is taken Selecting Settings button opens the LED Pulse Durations dialog box where the snap shot illuminator
30. n be controlled simultaneously Pressing the center button Stop with switch off all selected LED banks Focus These buttons will move the focus motor up or down to up down focus the image The focus motor will start at slow speed and then ramp up to high speed Lock The lock indicator LED on the front panel is green when the indicator SVM340 is in position The Lock indicator LED turns red when the SVM340 is in motion e g while the traverse is moving to a preset 2 8 Back panel connections Se vu Ext Illuminator E i NN 92999 TL ABCD The SVM340 back panel 15 2 8 1 Video output The video signal is output on two connectors a BNC connector with composite analog RS170 or NTSC video and an S video output compatible with most video cards and analog recorders It is generally recommended to use the S video for best image quality but some monitors without S video input may require the composite video signal 2 8 2 Digital inputs and outputs The four digital inputs and three outputs on BNC connectors provide TTL level communication with external equipment The inputs can be used to control or strobe the four LED illuminator channels or to trigger more advanced behaviors The outputs are selectable and include video timing information motion status information and several advanced programmable flags The inputs could be connected to digital experiment controllers like the LabSmith LC880 interlock switches sensors
31. ncluded with the device It is always a good idea to check with the manufacturer s website to make sure you have the latest drivers If you have purchased a RS232 USB adapter you will also need to install the drivers for this device Again the disk with drivers and instruction manual will be included with the product Your computer may need to be restarted after the video capture or RS232 adapter drivers have been installed 1 5 2 Installing uScope If your computer does not already have DirectX9 0 or greater installed you will need to install it before running uScope DirectX9 0 is free and available directly from Microsoft s website Most computers will already have this software installed To install uScope run setup exe and follow the on screen directions A dialog box will pop up that says Select a new serial port Select the COM port that the serial connector is connected to and click OK If you are not sure which com port you are connected to This dialog will keep popping up until you succeed in communicating with the SVM or you click Cancel then you work offline and uScope does not try to send commands to the SVM Communications properties x No response from SVM select new port Serial port COM1 wa Cancel Communications settings dialog bor Note Some functions are available with the SVM in offline mode Manipulation of the stage x y and z and illuminator settings can be accomplished via the fron
32. nsities to the values of the stored settings To store a traverse position press one of the storage buttons and hold it down a few seconds until the button light goes off This will store the current traverse position and the LED settings in the selected storage cell Note There are a total of 10 preset positions available on via the uScope software In LIGHT mode the buttons A D represent four LED channels labeled A D The 24 LEDs in the illuminator module are divided into four channels which can be controlled individually When a LED bank is selected the corresponding button lights up One or more LED banks can be selected simultaneously by pressing the one or more of the A D buttons Note When an EPI Optics Module is installed in the SVM the EPI illumination is controlled using front panel button D In this case illuminator channels B and D are both controlled by front panel button B In SITE mode the four buttons will move the traverse in the x and y directions Pressing a button will start the traverse motor at low speed and after about two seconds motor speed slowly ramp up to high speed Pressing the button briefly allows single stepping of the traverse Pressing the center button Stop will immediately stop any traverse movement which may be in progress When in LIGHT mode the up down keys will increase decrease the intensity of those LED banks which are selected by the A D buttons One or more of the LED banks ca
33. on 5 Click the and toolbar buttons to make the probes more or less transparent The software will continue to calculate velocity at these locations even if you make the probes completely invisible 6 To remove a probe right click on it and choose Delete When you first create a probe uScope will experimentally determine the fastest FFT algorithm to use This process may take up to 60 seconds to complete at which point the software will begin calculating velocity at the location When you create a probe it will take on the properties of the last probe you altered Once created you can change each probe s properties individually 7 1 3 Velocity Probe Properties 1 Double click on a probe to open the PIV Probe Properties dialog box You can also right click on the probe and choose Properties to open the dialog box 45 Subimage size Width Height 28 v x 128 pixels Averaging percent per frame 0 none Background mean rms 33 Correlations auto cross 95 Calculation options Time interval 12 frames 1 use consecutive images 4 Subtract mean Deconvolve autocorrelation Display options v Show field Cross correlation Show text Show vector Scale 5 M v PIV Probe Properties dialog box 2 Select the Width and Height of the probe window the area over which statistics will be calculated Some guidelines for setting the probe window size are a Pro
34. ont panel controls or through the uScope application software included with the instrument 1 1 New in uScope V Version 1 026 Version 1 026 of uScope software includes a number of new features and improvements to existing features Motion limits Motion limits on the XY stage are useful if you have installed a device on the SVM i e a chipholder that may interfere with the stage at its preset limits Snap shots The snap shot feature lets you create a single image consisting of an average of one or more consecutive images Time lapse The Time lapse option lets you select the frame rate frequency to allow video taken over a long period of time to be compressed to a small file and played back at increased speed Video compression Though uScope does not have built in compression it can now use video compressors that are installed on your computer To add compression functionality you need to download and install a codec A compatible codec will also need to be installed on anything that plays the video Deinterlacing Improvements have been made to the deinterlacing method and to the Deinterlace Settings dialog box Buffering Improvements have been made to the method by which video is buffered to RAM memory The newest version of uScope software uses video buffering for the video recorded live not from the pre trigger buffer so that this video is also saved without dropping frames Recording a video Improvem
35. or other external devices and the outputs connected to other apparatus to facilitate real time control and automation 2 8 3 External Illuminator This male nine pin D sub connector provides 5 V DC power and pulse signals to drive 4 external illumination sources with settings similar to the four bank led module Pin connections 5 V DC max 3 A 2 Chassis Ground 0 V 3 Chassis Ground 4 Chassis Ground 5 Chassis Ground 6 LED A drive TTL 7 LED B drive TTL 8 LED C drive TTL 9 LED D drive TTL 16 The light intensity of the SVM340 LEDs is controlled by pulse width modulation with a freguency synchronized to the video signal Full light intensity means an illumination duty cycle close to 100 LED drive outputs A D are negative logic i e TTL level is high when LEDs are off 2 8 4 RS232 serial connector The female 9 pin D sub connector is for RS232 communications This link allows the SVM340 to receive programming and commands from an external controller e g a computer running the uScope application or LabView through the provided serial cable A USB RS232 converter can be used for computers without an RS232 connector COM port 2 9 Microscope stage The SVM340 is fitted with a replaceable microscope stage attached to the main body of the instrument by four magnetic locks To remove the stage simply pull the stage gently up until it releases The stage top is
36. or the USB video capture device For the later then plug the USB video capture device into a USB port Most of the access to the SVM340 features will go through the uScope application software You can also however access some important functions directly from the front panel 12 Storage buttons LED selectors Lock indicator LED Site light Toggle buttons N Keypad ATI e LETT m j Focus control SVM340 front panel 2 7 Front panel controls The Power button and Power LED are located in the upper left corner of the front panel When the power is turned on the LED will flash green and red while the system runs its initial tests and turn green when the tests have passed Site Light These buttons toggle between SITE mode and LIGHT mode When the SITE button is lit the four storage buttons A D represent four different stored positions and the keypad controls the traverse movements The focus buttons moves the objective up and down for focusing When the LIGHT button is lit buttons A D represent the four LED channels and the keypad up and down buttons control the intensity of the LED banks selected by the A D buttons A D In SITE mode the buttons A D represent four stored 13 Keypad 14 settings of the traverse and focus positions and LED intensities To recall a stored position select SITE mode and press and release a storage button The traverse will move to the location and set the four LED inte
37. probes 7 1 Velocity PIV probes uScope software makes it easy to create probes to monitor flow characteristics Each probe can have its own properties probes are almost always square though it is possible to extend the probe in one direction to increase signal to noise ratio along that axis TIP When learning how to use uScope s PIV probes it is useful to start with a stable particle flow or a movie of a stable flow 7 1 1 Setup 1 Connect the SVM to the computer and turn on both 2 Launch uScope software 3 Prepare the microfluidic channel Fill it out with the buffer and introduce a sample of polystyrene fluorescent particles 4 Adjust focus illumination and flow characteristics Alternately you can also open an existing flow movie by choosing Video gt Process Saved Video Creating velocity probes 7 1 2 Creating a PIV probe To create a probe 1 Click the Velocity Probe toolbar button E to highlight the button 2 With your mouse curser over the image right click on the mouse and select New Probe Bring the mouse to the center point for the new probe and left click the mouse to place the probe A probe such as the one below will appear 44 New probe showing correlation field vector arrow and real time velocity as text 3 Repeat step 2 to create as many probes as desired Once created the probes can be moved by clicking and holding the mouse button over the probe and dragging it to the desired locati
38. r magnification generally have insufficient stand off distance to clear the illuminator LED s and can only be used with an external illuminator module or other external light source WARNING Dust particles can enter the optics module when the objective is not installed Removal or changing of the objective should be done in a clean environment when possible We recommend that a piece of tape be placed over the objective opening if the optics module will be stored without the objective installed Objective and seat for fluorescence filter 2 5 Fluorescence filter The fluorescence filter can be installed in the B amp W and Color camera modules The filter is installed by removing the objective and carefully 11 placing the filter in the recessed opening A compliant washer provided with the filter is placed over the filter to keep it secure under the objective Note The EPI camera module is supplied with pre installed fixed filters that cannot be removed 2 6 Base stand Power plug the power cable from the back of the SVM340 into a 90 240 VAC power outlet Communications connect the 9 pin D sub serial connector on the back of the SVM340 to a free serial port on the PC You may use a USB RS232 converter device if your computer does not have a RS232 port Video the connect the s video cable to the S video input on the back of the SVM and into either the s video port on the video capture card installed in your computer
39. sed speed The time lapse options are set by clicking on the Time lapse button W Time lapse at the bottom left side of the main window The Time Lapse Settings dialog box will appear Save images that have 9 Frames been averaged for C Miliseconds Skip frames so a video image 39 9 Frames is saved at most every Milliseconds ox ances Time Lapse Settings dialog box If averaging is desired check the top option and select the number of frames or miliseconds to average The resulting file will have an apparent increase in speed equal to the number of frames averaged images If frames are to be skipped check the bottom option and select the number of frames or milliseconds to skip A setting of 1 indicates one frame is 41 skipped between each captures frame The resulting file will have an apparent increase in speed egual to the number of frames skipped between images 1 If both options are checked the set number of frames will be averaged then the set number of frames will be skipped resulting in an apparent increase in speed of the frames averaged the frames skipped 6 9 Distance indicator The Distance Indicator feature allows you to measure features on your image To create an indicator es 1 Click the Distance Indicator toolbar button button 2 With your mouse curser over the image right click on the mouse and select New Probe Click on the image to insert the indica
40. settings can be selected After the 36 snap shot is complete the illuminator will switch back to the original settings Cancel LED pulse duration dialog bor This function is useful to prevent photobleaching or heating of your sample With this option the illuminator is typically turned off or very low prior the snap shot Frames to delay before averaging Choose the number of frames to skip after the snap shot button is selected and before it takes the photo File naming This option allows you to set the default for the type of file compressed jpg or uncompressed bmp and the naming The files can be autonamed or you can choose to be prompted each time to choose the file name This window can also be access from File gt Snap Shot File Saving 37 Type of file Compressed bitmap images ipg Y Do not auto name prompt for name Auto name files File path and name root C Users Eric Cummings Documents uS cor Append the date YY MM DD Append the time HH MM S5 J Append counter starting at 10 Example C Users Eric Cummings Documents uS cope Files SVMO00010 jpg Naming settings for snap shots 6 7 Deinterlacing The camera built into the SVM340 runs in standard RS 170 monochrome or NTSC color video format at a fundamental frame rate of 30 Hz As discussed in section 5 1 the full video frame is composed of two interlaced fields at a field frequency
41. t panel Images can be viewed and recorded with the SVM operating offline however real time measurements PIV and Intensity probes are disabled 2 SVM340 HARDWARE The following section describes how to set up your SVM and how to use it independent of the uScope software 2 1 Feet The SVM340 is shipped with the feet removed to protect the unit during shipping They must be installed on the unit before an optics module is inserted Note The SVM uses a sheet metal chassis to minimize weight and cost The sheet metal chassis occasionally can have some unevenness that causes it to rock when the feet are attached The feet are designed to have some adjustability to accommodate for this unevenness This unevenness does not affect the function of the SVM due to the kinematic design of the focus stage 2 2 Illuminator module The illuminator module consists of four independent LED channels Two of the channels A and B have 8 LEDs each and two channels C and D have 4 LEDs each Available LED colors include Color Wavelength range Blue 464 476 nm Green 520 535 nm Red 615 636 nm Yellow White Standard illuminator modules Name Channel A Channel B Channel C Channel D LED B blue blue white Blue LED G Green Green White Green LED R Red Red White Red LED Y Yellow Yellow White Yellow LED W White White White White LED X Blue Green White red LabSmith can provide
42. terlace Video options dialog box The best deinterlace filter depends on the nature of the video image and should be chosen by experimentation A brief description of the three most common algorithms is given here Weave This method uses three fields in the calculation and works well on slow moving material but tends to fail on fast moving material Bob The basic bob algorithm uses the most recent field and fills in the lines between by interpolation This method detects weaving artifacts in the current image it uses bob to get rid of them This method has a tendency to bob rather too much and gives poor results on fine static images Two frame This method uses the current frame and the last two to determine whether to bob or weave a given pixel This gives better results 40 on both stationary and moving images than the above two methods but uses more CPU Although the deinterlace filters improve the visual appearance of the video they are not always effective for scientific imagery All filters are based on some form of interpolation between frames under the assumption that scene motion is continuous between frames When the movies are analyzed by various algorithms the effect of the deinterlace filter on the result will be algorithm dependent 6 8 Time lapse The Time lapse option is used to select the frame rate frequency to allow videos taken over a long period of time to be compressed to a small file and played back at increa
43. the red dot will move outside of the window and uScope will not be able to measure the velocity In this case increase the window size which will improve the signal to noise ratio b Autocorrelation is an indicator of resolution The mass at the center of the window will become sharper with smaller particles and better focus c Mean shows the data that is being subtracted as part of the Background based upon the Background described above Showing the Mean can be helpful for highlighting stuck particles and other anomalies in the flow d RMS is an indicator of the amount of useful signal available for the calculations e Show Text turns on and off the text based velocity display f Show Vector displays an arrow in the direction of the flow The size of the arrow will change with velocity You can also set the Scale to increase or decrease the arrow size 7 2 Intensity probes Intensity or polygon probes are used to track the color spectrum or fluorescence intensity inside a defined region 48 7 2 1 Creating intensity probes To create a probe 1 Click the Intensity Probe toolbar button I to highlight the button With your mouse curser over the image right click on the mouse and select New Probe Click on the image to draw the outline of the probe When the shape is defined double click the mouse to close the polygon A probe such as the one below will appear START Sey aAA SX ERIT e E A 4 57 Soh ial NP
44. tor The ends of the indicator can then be moved click and drag to the desired locations to highlight the Note The distance calculation is based on the magnification setting for the objective If the magnification setting is incorrect the 42 distance will be incorrect If you are evaluating a saved image you will need to know what magnification was used and adjust the magnifiction at SVM gt Magnification gt 3 Repeat step 2 to create as many indicators as desired Distance Indicator display data can be selected by selecting the probe left click then right click and select Properties The following dialog box will appear Aa Distance angle indicator properties o A End to end distance 252 41577 um Angle 30 degrees Display options Color Red Green Blue 255 255 0 Line thickness 2 pixels IV Show end bars VI Show distance F Show angle Distance angle Indicator Properties dialog box 7 PROBES uScope has sophisticated real time probe capabilities that allow users to monitor image properties like color intensity variation and video properties like inferred motion e g particle image velocimetry in real time These real time measurements can be recorded to disk and can 43 trigger real time actions uScope can support as many probes as your computer s processor can handle The two types of probes that can be made in uScope are the Velocity PIV probes and Intensity
45. value improves noise control 4 The Calculations Options control how the flow parameters are calculated a Note Enter 1 in the Time interval box to calculate cross correlation for every sequential pair of frames Enter 2 to use every other frame 3 for every third frame etc This option is useful for examining very slow flows Subtract Mean subtracts the background non moving data from the flow calculations The amount of data that will be subtracted is based on the Background value see above If the probe is located in an area of very slow flow then subtracting the background could delete active particles Deconvolve Autocorrelation is an advanced option for high precision measurements This option deconvolves the cross correlation by the autocorrelation which can remove 47 the effects of blur and particle size such that each particle is treated as a single point It is most useful when the signal to noise ratio is extremely high 5 The Show Field options control which data are displayed for each probe window a Cross correlation determines how far the particles move between frames or between every few frames based on the Frames Skipped option This field is a good diagnostic tool to help you optimize experiment parameters The red dot will move further from the center as the flow velocity increases The dot should be small and well defined to achieve the most reliable measurements If the flow is too fast
46. w LabSmith TOOLS FOR SCIENCE SVM340 Synchronized Video Microscope User s Guide uScope software 2009 2012 LabSmith This manual 2012 LabSmith No part of this document may be reproduced without the written consent of LabSmith Table of Contents 1 INTRODUCTION 3 1 1 New in Version 1 026 cereus 3 1 2 Package contents ooi seo ias manini Ga uuu n nua SUR GR US 4 1 3 Basic TUNCONS iuoioe dodo sasa sasa na ra dara da re gera ia ne do Ua de ce daa sas 5 1 4 Computer requirements eeeeeeeeee 5 1 5 Installing the software 6 2 SVM340 HARDWARE 8 UM QT Ce 8 2 2 Illuminator module iscxa exiens ex sexin eru sex neri pita eir ens 8 2 3 Optics module eren rcv cea ia 10 2 4 Microscope objective uuu 11 2 5 Fluorescence filter 11 2 6 Base stand oes esi esi esu anus usu ioina anisan 12 2 7 Front panel Controls ouais eios seii secant sara na sana ra nasa n arasds 13 2 8 Back panel connections 15 2 8 1 Mide UD ua bestes eite 16 2 8 2 Digital inputs and outputs eei pecie etacioi petuo ed 16 2 8 3 External Iluminatot iie etait ee omoes atto nausea Du 16 2 8
Download Pdf Manuals
Related Search