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FAQ

FAQ

  • Which Windows version is the FluorCam 7 software compatible with?
    It is compatible with Windows XP, Windows Vista, and Windows 7 (32 bit versions only).
  • Which LED panels are mounted in the standard FluorCam?
    There must be two pairs of panels - each pair of the same color. The standard setup is: two red-orange panels 618 nm providing Measuring Light and Actinic Light 1. The second pair generates Actinic Light 2 and Saturating Pulse. These panels may be either white or blue 455 nm or red-orange 618 nm.
  • How should I make choice between white, blue or red color for the second pair of panels (Actinic Light 2 and Saturating Pulse)?
    Blue actinic light is often used in the systems where GFP fluorescence is detected together with Chlorophyll fluorescence and blue LED panel (450nm) is used as excitation light. For chlorophyll fluorescence kinetic measurements both blue and white panels can be used. In case of blue panel one wavelength light source is used to active photochemistry (450+/- 10 nm), in case of white panel, the spectrum is covering large proportion of the PAR range. Thus it is up to your decision which of the light source would suite more to address your research questions.
  • Can you also add a UV panel to my FluorCam?
    Yes, we can supply an additional UV panel that is mounted around the camera. It is constructed with 4 LEDs, their wavelength is 365 nm or 385 nm, according to the customer's preference.
  • What is the meaning of Fv/F, Kautsky, Quenching, Dyes and Fps?
    Fv/Fm is a short protocol giving you Fo, Fm, and maximum quantum yield of Photosystem II = Fv/Fm. Kautsky kinetics is a fluorescent transient measured in continuous actinic light – so called Kautsky effect. Quenching analysis is a complex protocol giving full information of dark adapted as well as light adapted state of the plant. There exist some good reviews e.g. Maxwell, 2000 - http://jxb.oxfordjournals.org/content/51/345/659.full.pdf. Dyes and FPs is a special protocol for measuring GFP and other FPs.
  • What is usual value of Fv/Fm in a healthy plant?
    Fv/Fm of a healthy plant is 0.83. If it is lower, the plant might be stressed. However, be aware of correct measurement of Fv/Fm. The saturating light must saturate photosyntesis and measuring light must be weak enough to determine correct Fo without actinic effect.
  • Is there any possibility to assess the chlorophyll concentration using the FluorCam?
    Yes, this is possible with the PAR Absorbance Module (includes the filter-wheel, quartz filter and additional "PAR" light panel with 670nm and FAR LEDs. Using this module, you will be able to measure also Chl concentration heterogeneity. Easier and cheper solution might be if you use the PSI's PlantPen http://psi.cz/products/pocket-sized-instruments/(no heterogeneity comparison).
  • Using data export in the FluorCam, is it better to use "frame numeric" or "numeric average"?
    In general, we would always recommend to use numeric average. FvFm measurement can serve as an example for explanation. If frame numeric is used, you use pixel by pixel fluorescence values to calculate FvFm and then you average the FvFm value over the area that you selected, means over all pixels selected. In case of numeric average, you take Fo value over all area selected (all pixels selected) and Fm value over all area selected and use this F0 and Fm value to calculate FvFm. If you analyse object with strong signal and you do not integrate any noise, you will not see any difference between the two results. If you have weaker signal and you have some noise in your measurement, the average numeric will be always more powerful with less noisy pixels included.
  • Sometime my fluorescence data from the FluorCam show "pixel overflow", what does it mean? How does it affect my data interpretation? How could I fix it?
    Range of fluorescence units that can be detected by the camera is 0-4096 units. Any signal exceeding the maximum CCD well capacity (4096 levels) is indicated by the warning pixels overflow. Always prior initiating new experiment you need to adjust the settings in live window or protocol window as shutter, sensitivity and light intensity as such that when the given light used with the given settings (shutter and sensitivity) is for your imaged plant material giving fluorescence signal in 1/3 of the CCD well capacity meaning about 1500 units. It also must be taken into account that for different plants (for example less chlorophyll vs dark plants) different setting might be required and will have different response.
  • How does "electronic shutter" and "sensitivity" affect the imaging quality? Should I modify it for each condition? What combined settings do you recommend for best result?
    Please refer to the manual provided and page 41, where you can find description how to define correct settings for measurements. In short: the shutter opening determines the duration of the interval during which the electronic shutter is opened during measurements. It controls also the duration of the measuring flashes and that cannot be longer than 20 or 30 ms. The apparently brighter measuring light with longer shutter opening time is due to the longer on-time rather than to an increased photon flux. The brighter fluorescence signal with longer shutter opening is due to longer integration in the CCD chip. The higher signal and the better signal-to-noise ratio with longer shutter opening time is unfortunately traded by increased actinic effects of the measuring light. The measured signal deviates from the true Fo if the measuring light is too strong. The problem can be alleviated by low repetition frequency of the measuring flashes. The sensitivity scale is linear and relative (0-100%): 0 meaning minimum sensitivity and 100% meaning maximum sensitivity. The maximum sensitivity range (80-100%) should be used only when necessary, because it can lead to a relatively low signal-to-noise ratio. Optimal setting for the sensitivity would be in range 0-50%.
  • We are using the FluorCam system for our measurements very successfully. Is there a way to export the fluorescence/time data from a Kautsky measurement beside the preset parameters (Fo, Fm, QY etc.)? The data is shown for each experiment in the software (FluorCam 1.0.6.14) very nicely. But we need to compare multiple data sets from different experiments.
    There are two ways how to do it: (1) To export the raw data (fluorescence transient - graph), please go to: EXPERIMENT (top panel) -> Export -> Kinetic; (2) To export calculated parameters (Fo, Fv/Fm...): go to EXPERIMENT (top panel) -> Export -> Numeric. In both cases, it is recommended to select “All data“. For Numeric data: Frames numeric – are calculated for each pixel (e.g. Fv/Fm for each pixel) and then averaged over selected area. Averages numeric – first absolute parameters such as Fo, Fm, Fp... are calculated over selected area and then these values are used to calculate more advance parameters e.g Fv/Fm = (Fm-Fo)/Fm. The Frames numeric can give different (non-sense) values in the case of weak fluorescence signal with low signal/noise ratio. The data will be exported to txt file which can be easily imported to for example Excel.
  • How can I measure light intensity in the infrared LED Light Panel, which I use with my FluorCam?
    For wavelengths above 700 nm, is not possible to use standard PAR light meter and measure light intensity in µmol(photon).m-2.s-1. Instead light can be measured for its radiated power (output power is given in milliwatts).
  • I am considering purchase of your GFP-Cam, closed version. Do I need to order a High-Resolution Camera as a separate item?
    No, the High-Resolution Camera and motorized filter wheel with filters for GFP and Chl expression are included in the price of the GFP-Cam system.
  • Is it possible to use the FluorCam or GFP-FluorCam to detect Luciferase signal?
    Yes, it is possible to detect Luciferase but the standard FluorCam instrument (FC 800-C, FC 800-C-GFP) is not needed for this purpose. In principle, no LED panels and filters are needed because Luciferase emits light based on chemical reaction in contrast to fluorescence emission. On the other hand, a very sensitive cooled CCD camera is needed for Luciferase detection (this camera is much more expensive than the camera used for fluorescence imaging). To sum up, PSI is able to deliver the system for Luciferase detection. It would consist of a mechanical construction used for the FC 800-C, 1 LED accessory panel - allowing easy sample manipulation under the camera, cooled CCD camera and modified software.
  • Where can I check FluorCam program compatibility with different Windows versions?
    It can be checked at our web page http://psi.cz/downloads/
  • How can I use the advanced Multiple function in the FluorCam software?
    The Advanced Multiple function enables combination of two protocols and thus it is useful for circadian cycle study: one protocol runs at day time, the second protocol runs at night. This protocol is a paid one and must be purchased as an optional feature. The key to this protocol is then copied on delivered computer, directory: C:\Install...\Install CD\User Keys and on delivered installation flash disk, directory ...\User Keys. If the protocol is activated, you will see „double red flash“ icon in main tool bar of the FluorCam software.
  • Which Windows version is the FluorWin software compatible with?
    It is compatible with Windows XP, Windows Vista, and Windows 7 (32 bit versions only).
  • What is the detection limit of PSI Fluorometers?
    Sensitivity/detection limit of the fast fluorometer (FL 3500/F) is 1-5 ug/L of ChlA. Standard fluorometer (FL 3500/S) can be adjusted to detection limit 100-500 ng/L of ChlA (special type of protocol - multiple turnover flashlet sequence - must be used). High sensitivity fluorometer (FL 3500/HS) with integrating sphere can reach down to 1-10 ng/L of ChlA ( with multiple turover flashlet sequence protocol).
  • Does the Fluorometer control software run also under Windows 7?
    Yes, FluorWin, control software for Fluorometers, runs under Windows XP, Windows Vista and Windows 7. Program compatibility with different Windows versions can also be checked at our web page http://psi.cz/downloads/
  • Just recently I have bought your fluorometer FL 3500/F and now I am thinking about its upgrade. Will the Oxygen Detector be a good choice?
    Indeed, the Oxygen Detector with oxygen microelectrode is a very useful tool. In principle, it serves for detection of oxygen evolution. A user can program his/her own oxygen evolution protocols (using, for example, single turnover saturating flashlets). In such case, data from the oxygen probe are not temperature compensated and 2-point calibration for the absolute concentration must be done by a user.
  • I am looking for Qy, OJIP and FRR capabilities in an instrument that would offer 'normal' high sensitivity detection of fluorescein with a different LED for excitation and detection. Can the High-Sensitivity Fluorometer FL 3500/HS be used for such application?
    Yes, this Fluorometer can be very useful for your experiments. It offers scripting language for protocol definition (light actions, measurements, external triggering-pumping, etc.) and next to the predefined protocols like Qy, OJIP or FRR there can be executed also your own scripts. The masuring compartment is designed as an integrating sphere(40 ml volume) and avalanche photodiode detectors.
  • What is the most favorable location of the glass straw in the vessel of Multi-Cultivator MC-1000-OD so as to ensure a complete mixing of the culture: at the very bottom, at the the two-third...?
    The best position of the glass straw is on either side of the vessel (because the OD sensor is aligned with the center of each cultivation tube). Please, check that all cultivation vessels, silicone plugs and aeration glass tubing are at the same position. All aeration glass tubing should be the same distance from the bottom of the cultivation vessel. The position of the aeration tubing end affects the size of the bubbles. Optimal position of the end should be in about 0.5 mm from the bottom of the vessel. Ensure that there are no kinks in the silicon tubing that may impede the flow of gas. And ensure the end of the glass straw is sufficiently away from the bottom of the vessel not to hinder the bubbles coming out of the straw.
  • In the Multi-Cultivator MC-1000-OD, it is hard to apply exactly the same air flow in the different culture tubes, even by opening or closing the taps. So I take a look at the number of bubbles produced in each vessel and I adjust the taps in this way. Do you have any solution, less 'subjective', to fix this issue?
    Regarding the gas flow rate into each tube - you can install some mini flowmeters on the tubing between the taps and glass straws and try to improve the control of the flow rate a little bit. In general, the Multicultivator is a low-cost device and that's why it doesn't include precise control of the gas flow rate into each tube.
  • Can the Multi-Cultivator MC-1000-OD aeration unit (black metallic tube with 8 small valves) be autoclaved?
    The Humidifier (1L glass bottle with accessories) and silicone tubes can be autoclaved to 121°C. The black aeration tube with valves can be autoclaved to 75°C only. This tube can also be sterilized with 70% ethanol.
  • Can you provide more information on how the optical density measurements are performed in the Multi-Cultivator MC-1000-OD?
    The method is based on light absorption of certain wavelengths (680 and 720 nm) by chlorophyll and cell walls. Basically, we compare light intensity measured with/without sample in the test tube. The whole process of OD measurement is automated. You can either start it manually, or you can setup a protocol where OD measurement is performed in periodic intervals. Measured data can be later downloaded to a PC.
  • Is the water level in the Multi-Cultivator test tubes topped up automatically, allowing minimal user supervision?
    There is no automatic level detection in the test tubes, no medium is added during an experiment. The only substance coming into the tubes is humidified air, which along with condensation system grants minimal medium evaporation.
  • Can the User-Defined Custom Protocol for Multi-Cultivator be fully defined by the user (not needing to order programming from PSI)?
    Yes, a user does the programming all by himself. The protocol is created in a PC, as a text file with given syntax, and then uploaded to the device using provided software.
  • Regarding the (224 maximum) light phase intervals the User-Defined Custom Protocol for Multi-Cultivator; What is the minimum duration of a light or dark period? Can I program any sequence of light (any intensity and duration) and dark periods?
    The smallest time step is 1 second. Any sequence with maximum of 224 intervals can be programmed. Interval is defined by light intensity in percents of maximum and duration in seconds.
  • Regarding the User-Defined Custom Protocol for Multi-Cultivator; Can I define separate protocols for each of the different tubes, or the same protocol has to be applied to all tubes?
    Each tube is controlled separately by its own protocol.
  • It appears that the Photobioreactor system can only support either dCO2 or dO2 measurements, and not both simultaneously - is this correct?
    No, you can measure both dO2 and dCO2 simultaneously, but you need the CO2 module to do that.
  • It also appears that in the Photobioreactor, dCO2 and dO2 probes cannot be value-corrected within the software (output of sensor doesn't appear to be units of mg/l or mmol/l, although this can be corrected for offline measurements.
    For dCO2 you can put calibration constants in software and then the values are automatically recalculated to correspond umol/l units. This requires new version of PBR GUI. This can be updated remotely, but you need to have the Photobioreactor computer connected to the internet or you have to ask for an installation CD with instructions. With dO2 concentration we don't have it in the GUI since the calibration is more difficult due strong influence of environmental properties on solubility (such as salinity, temperature, etc.). Also there is significant influence of temperature on the probe electronic circuits resulting in changed sensitivity. All these effect has to be corrected by a user in data post-processing.
  • We are afraid of excessive evaporation from the Photobioreactor. Have you addressed this issue somehow?
    We are routinely using the gas humidifier (bottle with dH2O) on tubing line before each Photobioreactor.
  • What is the pressure rating of the Photobioreactor vessel?
    Operational pressure should be always below 0.25 bar.
  • Is there a chance to see how newPhotobioreactor software works?
    Yes, there are video tutorials in the Video Gallery on the PSI web site.
  • WhichPhotobioreactor panel (blue/red or white/red) works better for cyanobacteria growing?
    Cyanobacteria use phycobilins as additional photosynthetic pigments with absorption maximum in red region, therefore cyanobacteria are more sensitive to the red light and usually a combination of white/red light is recommended for cyanobacterial cultivation.
  • I plan to order a FytoScope FS-130. Can I order it with both temperature and light upgrades?
    No. From technical reasons, having both upgrades in one FytoScope is not possible.
  • We have a problem to activate the GPS Module. How can we activate it?
    Please check the Manual provided. To correctly attach the GPS coordinates, it is essential to set time correctly on the device and on the PC. It is using time zone settings from the computer so you should check that too. Also check that Garmin is set in Mass Storage mode.
  • Is the FluorPen / AquaPen software capable of recording used light intensitis?
    Unfortunately no.
  • Is there a function "RESET TO FACTORY SETTINGS" in the FluorPen / AquaPen software?
    Unfortunately, there is no such function in the FluorPen software. The only possibility is to reload the device firmware, which we recommend just in emergency cases.
  • What is measuring time of the FluorPen / AquaPen protocols?
    It differs for single protocols: Ft takes about 100 ms, OJIP and QY about 1-2 seconds, NPQ and LC protocols take up to few minutes.
  • Is it possible to calculate ETR from data measured by the PAR-FluorPen?
    Yes, it can be calculated by the Light Curve data using this equation: YII*PAR*0.84*0.5.
  • In which units is measured fluorescence in FluorPen / AquaPen devices?
    Fluorescence is measured in relative fluorescence units, also called arbitrary units.
  • Where can I check FluorPen program compatibility with different Windows versions?
    It can be checked at our web page http://psi.cz/downloads/
  • Is my FluorPen device equipped with both USB and Bluetooth communication?
    No, the device always comes with just one communication module - either USB or Bluetooth.
  • I have a FluorPen with USB communication and I need to download measured data to a computer. However, the computer does not recognize that the device is connected. Can you help on this?
    For USB connection you need to have the USB driver installed in your PC. You find the driver on the installation disk (USB driver folder). If you check the Device Manager in Windows you should see the USB serial port in the device tree. In case of missing driver you may download it from the following link: http://www.psi.cz/ftp/FluorPen/USB_Driver_Setup.exe When the driver is installed correctly you should be able to connect to the device in the FluorPen software menu Setup->Device ID.
  • I have a problem downloading data from our FluorPen. When the device gets to the end (100%) of the download, it gives an Error: TFpData:parse Data0 -> unknown ID 0. And then just sits with the spinning circle and there is no way to get data off the unit.
    This error means that the data in internal memory are corrupted. The reason for that could be for example power failure (battery dead or removed) during data saving procedure. If there are no important data it could be easily solved by erasing the memory.
  • Referring to the GPS Module - what is the accuracy of the location registration?
    It is a standard GPS with accuracy of +-2m. Current accuracy is influenced by signal strength and it is shown on the GPS device.
  • I have a FluorPen with USB communication. I transferred the measured data to a PC via the FluorPen software. Now I am trying to save or export it to txt format, but the Export icon at FILE menu is not functional (disabled ). Do you have an advice to enable the key and its function?
    You need to activate the software by entering the serial number. You can do it in the menu Help-Register. Your serial number is on the installation flash drive in the SN.txt file. The procedure is also described in the user manual.
  • What should I do when the display on my FluorPen shows just FP-Boot and 1.0.0.0 when switched on and does not do anything after that?
    Please update the firmware with the BXN file. Update procedure: (1) Connect the device to the PC; (2) Select menu Setup->device ID; (3) Select menu Setup->Update firmware from file; (4) Select the downloaded BXN file. Firmware updating procedure is also depicted in the Operation Manual.
  • We are unable to download the data from the FluorPen to the Excel spreadsheet: please, could you tell how can I do?
    In the Fluorpen go to Export and export the data to txt file. Then in Excel go to Data and Import Data from Text. In this way you export data directly to Excel and process then further. You can find more information on how to do it for example here: https://support.office.com/en-us/article/Import-data-using-the-Text-Import-Wizard-40c6d5e6-41b0-4575-a54e-967bbe63a048
  • Is it possible to export just part of measured data or all data must be exported?
    It is possible to export all data or one selected measurement. Mark the selected measurement by mouse before export. Then go to Export menu and choose Selected only.
  • Can I measure Ft and QY in presence of light (without dark condition)?
    Basically all measured fluorescence parametres can be acquired either after dark adaptation or in the light adapted state. Ft refers to Fo if the leaf sample is dark-adapted (Fo refers to minimal level of fluorescence in dark adapted state). QY measured in the light is equal to Fv´/Fm´ and it provides an estimate of the PSII maximum efficiency within light-adapted material in contrast to Fv/Fm which is an estimate of the PSII maximum efficiency within dark-adapted material. Explanation of particular parameters: Fo - minimum fluorescence signal (when all PSII centres are in the open state) from dark-adapted material; Fo' - minimum fluorescence signal (when all PSII centres are in the open state) from light-adapted material; Ft - fluorescence signal at any point between Fo' and Fm', in other words instaneous fluorescence which is affected by the level of light the object is exposed to; Fm - maximum fluorescence signal (when all PSII centres are in the closed state) from dark-adapted material; Fm' - maximum fluorescence signal (when all PSII centres are in the closed state) from light-adapted material.
  • Is it good to measure dark-adapted samples?
    It is recommended to measure dark-adapted samples. The dark-adaptation guarantees the same starting conditions before measurement of samples cultivated in different conditions. But what is more important you get better results (= higher photosynthetic performance), because in dark all reactions centers of PSII relax and are ready for incoming light energy. In light-adapted sample some of the reaction centers are saturated with the ambient light and therefore cannot accept all photons of the incoming light and you get lower QY value. You could of course compare QY values of light-adapted samples, but the result could be affected by light conditions before the measurement.
  • How long dark-adaptation time is recommended?
    Duration of dark adaptation depends on species, in general it is between 5 and 15 minutes.
  • Do the Ft values change within one measurement or between measurements? Should I do some kind of calibration or programming before measuring?
    The value can change slightly (in range 10%). If the change within one measurement is bigger, it is recommended to set the f_pulse intensity lower. Strongly increasing Ft value within one measurement means, that f_pulse is too strong and causes unwanted "actinic effect" (= photochemistry starts). Fluorescence measurements do not require calibration.
  • What is the purpose of the PAR sensor (Light Meter) in the PAR-FluorPen?
    Integrated Light Meter serves for direct digital readouts of Photosynthetically Active Radiation (PAR) in the range from 400 to 700 nm, the span in which plants use energy during photosynthesis. PAR is measured as Photosynthetic Photon Flux Density (PPFD), which is indicated by units of quanta (photons) per unit time per unit surface area. The sensor has a uniform response to photons within the 400 - 700 nm waveband.
  • Can you explain meaning of the 'f_pulse' in the FluorPen device?
    This function serves for setting of measuring pulses intensity. The measuring pulses are weak pulses, which are able to induce the minimal chlorophyll fluorescence (Fo or Ft). It takes only 30 µs and the maximum intensity is 3000 µmol photon.m^-2.s^-1. It means 30 µs * 3000 µmol photon.m^-2.s^-1 = 0,09 µmolphoton.m^-2 per pulse is the maximal intensity of the f_pulse.
  • Can you explain meaning of the 'F_pulse' in the FluorPen device?
    This function serves for setting intensity of the saturating pulse. Saturating pulse is able to induce maximum chlorophyll fluorescence (Fm). 100% of intensity equals approximately 3000 µmol photon.m^-2.s^-1.
  • Can you explain meaning of the 'A_pulse' in the FluorPen device?
    This function serves for setting intensity of measuring pulses. Actinic light is basically the ambient light in which the plants are growing. 100% of intensity equals approximately 1000 µmol photon.m^-2.s^-1.
  • In the FluorPen, Fv/Fm, Fv'/Fm' and qP from the OJIP test, I can easily have the Fv/Fm value. Then for the Fv'/Fm' (thus the light adapted quantum yield of PSII) which values should I use (is it calculated or not)? Also for the qP (proportion of open PSII, [Fm'-Ft/Fm'-Fo']) is there any value coming out from the tests or should I calculate it by myself (or from the NPQ test?)?
    During OJIP curve measurement you do not use any light adaptation phase and therefore it is not possible to obtain PSII efficinecy in light adapted state and qP. OJIP is fast measurement of variable fluorescence transient during saturation pulse. To obtain Fv'/Fm' and qP you will need to use either Light Curve protocols or NPQ protocol.
  • We carried out several NPQ tests, but from the FluorPen datasheet I am not able to discriminate which is the NPQ value (Fom-Fm')/Fm'. Please could you explain to me a bit better what the data sheet from the NPQ means?
    There are quite some explanations regarding each of the protocols available in the Fluorpen in the manual. For the NPQ you should refer to the page 35. You can find also description of the parametres measured and calculated. NPQ is calculated as (Fm – Fm_Ln) / Fm_Ln. You obtain NPQ value calculation for each of the Fm´value measured by saturation pulse during light and dark adapted state.
  • Should the Light Curve and OJIP protocols be done after a dark adaptation?
    It is recommended to dark-adapt the samples before the chlorophyll fluorescence measurement. Duration of adaptation depends on the plant species, but in general 15 minutes should be sufficient. More information about the NPQ protocol can be found in the Operating Manual, page 32 – 36. Here are explained all parameters of this protocol. OJIP measurement reflect the chlorophyll fluorescence induction kinetics. O, J, I, and P steps correspond to the redox states of PS II and PS I and to the efficiencies of electron transfer through the intersystem chain to the end electron acceptors. If you want know the efficiency of the photosystem, you should better measure the Fv/Fm parameter.
  • In the FluorPen, I run few light curve tests (is the only one where I can see the Ft value): now, to calculate the ETR, I used the YII*PAR*0.84*0.5 equation (thus is giving me the response curve). Is that right? Thus, should I use the QY L value at each step (1-2-3 etc.) for each light intensity (i.e. for LC 2 is 0, 100, 200,300,500,1000 referring to QY max, QY L1, QY L2, QY L3 etc.)?
    Exactly, the QY_Lss (YII) is calculated as (Fm_L – Ft_L) / Fm_L . ETR is calculated exactly as you wrote: YII*PAR*0.84*0.5.
  • Is there correlation or conversion between SPAD and NDVI index that is measured in the PlantPen NDVI-300?
    There is strong correlation between SPAD and NDVI index, yet no direct conversion is possible. But both measurements refer to the same physiological information about the plants.
  • What is expected number range for PRI measurements in the PlantPen device?
    The range of PRI is -1 to +1.
  • What is meaning of functions: Multiplication and Average in the PlantPen Setting Menu?
    Multiplication is for obtaining the multiplied results. Multiplication could be x10, x100, x1000. It means, the result is PRI = 0.0523 when multiplication is set 1x, PRI = 0.523 when 10x, PRI = 5.23 when 100x and PRI = 52.3 when 1000x. Average measures the sample defined times (eg. 25x) and makes the average values from these 25 measurements. Higher the average value, then longer is the measuring time (but still it is couple of seconds). It could be useful for getting more precise results.
  • What is meaning of functions A and B, which appear in the measuring process in the PlantPen?
    It means the reflectance values at 531 nm and 570 nm from which the PRI parameter is calculated (PRI = (R531-R570)/(R531+570)), A = R531 nm; B = R570.
  • Is it possible to measure only Chlorophyll A with the AquaPen-C?
    The AquaPen measures Chlorophyll A and Chlorophyll B together. Excitation lights are 455 nm and 620 nm, emission band is 660-750 nm.
  • We received the AquaPen-C with a calibration certificate. Does it mean that the device is calibrated for both the optical density and chlorophyll content?
    In our testing laboratory, each AquaPen-C is calibrated for approximate chlorophyll content in suspension. We use our internal quality standard in which the OJIP measuring protocol is applied. The calibration is performed both for blue light (testing is done with green alga Chlamydomonas reinhardtii) and for red light (used is marine cyanobacterium Cyanothece). We do not perform optical density calibration since our customers prefer doing their own calibration on the specific organisms they are investigating.
  • In the AquaPen-C there is a function CAL. OD. How long it takes to execute once? For calibration, should I put the cuvette in the slot, blank or filled with water?
    If you want to measure the optical density, OD calibration should be performed after every swich ON of the device, because the previous calibration is not saved in the device memory. To get the most accurate results, we recommend to do calibration with the same cuvette using the same orientation which will be used for measurement. Calibration should be performed with distilled water or with cultivation medium. To check if calibration was done well, measure OD680 and OD720 of the calibration liquid (distilled water or medium). The result should be max 0,0003. If it is higher, perform the calibration again.
  • How should I adjust the measurement when I get „over-flow“ error message during ChlF measurement in the AquaPen?
    The „over-flow“ error message means that the ChlF signal is above the range of detection. The sample is too concentrated and should be diluted. As an example: For standard type of culture such as Chlorella vulgaris with OD 680 of 0.1 and AquaPen pulse setting of f_pulse 30%, F_pulse 70% the ChlF measurement can be measured correctly without any overflow error warning.
  • How should I adjust correctly the f-pulse (measuring flashes) settings prior to measurement with the AquaPen?
    The optimum value of f_pulse can be identified for instance with the QY measurement. Before initiating the QY measurement it is recommended to set the pulse color based on the type of measured culture (Algae or cyanobacteria) and intensity of F_pulse on 70%. QY measurement should be performed with dark adapted culture. If you use the cuvette version of the AquaPen, make sure that you use always fresh 4 ml of culture for each individual measurement (culture can be inhibited after measurement) or you wait given period of time between the individual measurements (to ensure relaxation of photosynthetic apparatus during the dark adaptation of the sample prior next measurement). The f_pulse setting recommended by the manufacturer is 30%. You can increase the intensity of f_pulse in case your culture has very low density. Please note that high intensities of f_pulse can cause undesirable “actinic effect” resulting in increase of F0 value - in this case F0 isn´t real dark adapted F0 and QY value will be lower. The f_pulse intensity at which the highest value of QY is reached is the optimal one for your culture.
  • How should I adjust correctly the F-pulse (saturation pulse) settings prior to measurement with the AquaPen?
    The best way to recognize the optimum intensity of F_pulse is to perform OJIP measurement. During OJIP measurement solely F_pulse (saturating pulse) is used for ChlF measurement. OJIP measurement should be performed with dark adapted culture. If you use the cuvette version of the AquaPen, make sure that you use always fresh 4 ml of culture each individual measurement (culture can be inhibited after measurement) or you wait given period of time between the individual measurements (to ensure relaxation of photosynthetic apparatus during the dark adaptation of the sample prior next measurement). The F_pulse setting recommended by manufacturer is 70%. The F_pulse intensity at which the highest value of Fv/Fm is reached is the optimal one for your culture.
  • Can I measure chlorophyll concentration in the AquaPen-C, and at which range?
    In the AquaPen-C, chlorophyll concentration is based on optical density measurements at 680 nm. Minimal chlorophyll concentration which you can measure with this device corresponds to 0.5 µg chlorophyll/L. The upper limit is defined by the principle of OD measurement and the fact that values over OD 680 nm are influenced by large error of measurement.
  • How big is the memory in AquaPen and FluorPen devices? How many OJIP curves can be saved in the device internal memory?
    About 1100 OJIP curves can be saved at one time.
  • How is defined optical density in the AquaPen-C?
    It is defined as OD = -Log(I/Io) where Io is the irradiance that is transmitted through the cuvette filled with medium without algae or other organisms. This quantity must be measured as the reference. I is the irradiance transmitted through the cuvette with algal or cyanobacterial suspension in which OD is measured. Log is the decadic logarithm of the I/Io ratio. Thus, optical density OD = 1 means that light at the respective wavelength is attenuated by algae or cyanos 10 times relative to the reference. With OD = 2, the attenuation relative to the reference is 100 times.
  • What is maximum light intensity that can be measured by the SpectraPen LM 500 light meter?
    Intensity up to 5,000 umol/m2/s can be measured.
  • Does the SpectraPen LM 500 use a CCD-chip or Prisms monochromator?
    It uses a Polychromator with CMOS linear image sensor.
  • In SpectraPen LM 500 , what is the average light sensitivity per channel?
    The integration time of the sensor is automatically adjusted between 5ms up to 10s to accurately measure the light intensity between 1 umol m−2s−1 up to approx. 5000 umol m−2s−1.
  • Can SpectraPen LM 500 measure the intensity of light individually for pre-selected parts of spectrum?
    Yes, one pre-selected part of spectrum can be measured at one time.
  • Can you shortly explain the difference in between the PolyPen RP 400, SpectraPen SP 100 and SpectraPen LM 500 ?
    PolyPen RP 400 measures reflectance on leaves or other plant samples. It is capable of calculation of various reflectance indices (some of them are pre-programmed). It features an integrated light source and a leaf clip. SpectraPen SP 100 is a spectrometer without spectroradiometric calibration. It features a SMA905 light fiber port. It is intended for measuring reflectance, transmitance and light wavelength. SpectraPen LM 500 is a spectroradiometrically calibrated spectrometer with integrated cosine corrector. It measures absolute values of light intensity in uW/cm2/nm and photon flux density in umol/m2/s/nm. It calculates: irradiance (uW/cm2/), PAR (umol/m2/s), illuminance (Lux), CIE1931 coordinates, CCT (L).
  • In the PolyPen RP 400, besides the different indices we get different Excel spreadsheets with: Spectrum / Spectrum Scope / Spectrum Absorbance / Spectrum Transmittance. But no reflectance?
    Export options in the software are related to calculation not the physical measurement setup. We are using the same software for multiple SpectraPen versions and thus not all options may be active in the PolyPen. Here are short descriptions of the export options: Spectrum - raw data with separate dark and reference spectra; Scope - scope data with dark subtraction (not in PolyPen); Transmitance - transmitance = I/Iref; Absorbance - absorbance = log Iref/I. Reflectance is calculated the same way as transmittance (it is not measured through a leaf).
  • Can we measure transmittance and absorbance with the PolyPen RP 400?
    Polypen is measuring reflectance. Transmittance/absorbance may be calculated according to this formula: T=I/I0 or A = log I0/I.
  • Is the reflectance standard used in the PolyPen RP 400 calibrated?
    No, it is not calibrated but the error is less then 2%.
  • How can I clean the reflectance standard used in the PolyPen RP 400?
    Please see the video on https://www.youtube.com/watch?v=SK4M_3Ck2ms or check instructions on https://www.labsphere.com/site/assets/files/2568/spectralon-material-care-and-handling.pdf
  • How can we synchronize PolyPen RP 400 and GPS measurements made in field?
    GPS logger is tracking the position automaticaly every 1 second, you dont have to do anything. The data and position is then synchronized according time in the PC software. Time must be properly set in both devices.
  • What is the maximum reading number we can measure with PolyPen RP 400?
    Maximum raw value is 65535. The sensitivity is set automaticaly during calibration so you don’t have to worry about it.
  • What is lifetime of the LED used in the PolyPen RP 400?
    LED lifetime depends on the frequency of usage. Under normal conditions it exceeds 5 years.
  • Can I obtain trustworthy results when measuring with PolyPen RP 400 or PlantPen if my plant samples are small, smaller than the optical entrance of these devices?
    Yes it is possible to measure smaller leaves with minor limitation. The leaf clip is equipped with white coating that is used for calibration. When you use smaller leaves the white coating become "visible" for the instrument and influence the results. This can be fixed by putting some black material as a background for the leaf to cover white coating during measurement.
  • How can I program my own index in the PolyPen RP 400 ?
    If you want to calculate your own index, you can of course do it from the raw data in Excel or you can add this formula to the Config/Formulas.txt in the PolyPen program folder. Syntax is very simple, for example: Transmitance:CRI2:Caroteniod Reflectance Index 2:1/Transmitance[510nm]-1/Transmitance[700nm]. Each parameter is separated with colon: the first one is data set which will be used as source data (leave there Transmitance); the second is name; the third is description and the last one is calculated formula. After you edit the Formulas file, restart the SpectraPen software. Your index should appear in the list and also in the exported data.
  • Does the PolyPen RP 400 work also on monocot leaves with a prominent midvein?
    The PolyPen should work as well on monocot species, basically with the similar principle as the NDVI and PRI PlantPens are working. These devices have been tested and used for monocot species. However it is important to remember that veins can indeed cause some interferences during the measurement and that the first leaves of same age should be cross-compared and, in an ideal case, the method should be standardized to the same part of the leaf.
  • What is difference in use between the white and black leaf clips in the PolyPen RP 400?
    Black leaf clip is limiting the measurement to reflectance only and it is preferable. White leaf clip is for transmittance measurement (actually it is a combination of reflectance and transmittance). It could be useful for some application.
  • Can you explain function of cosine corrector in SpectraPen SP 100 ?
    Standard SP 100 has a connector for attaching light fiber (SMA905). If you don’t attach anything on this connector, there is a small angle in which light is accepted by the instrument (what the instrument sees) - it is about 30 degrees. Cosine corrector is used for collecting light from 180 degrees angle. It is used for relative and absolute spectral intensity measurements, for emissive color applications, and for evaluation of light sources such as LEDs and lasers. Usage is optional and the corrector can be connected or disconnected very easily.
  • Is it possible to measure light source spectrum with the PolyPen or just with the SpectraPen?
    Light source spectrum can be measured just with SpectraPen; PolyPen is measuring reflectance.
  • Is there any difference in measuring absorbance and transmittance with the PolyPen and with the SpectraPen?
    PolyPen is equipped with an internal light source. Thus it is a complete system for leaf reflectance measurements not requiring any additional accessories. SpectraPen is a simple spectrophotometer with no in-built light source.
  • Are nitrogen values measured and displayed in % in N-Pen N 100 given in absolute or relative values?
    N-Pen measures nitrogen content in plant dry matter (in %) and predicts protein content in grains (in %). The measurements are precise if second youngest leaves are measured at mid-tillering.
  • I understand that the N-Pen N 100 device does not provide formulas of relative nutrition state for each growth stage and corresponding nitrogen nutrition recommendations. But can you at least provide with a prediction of nutrition state?
    Yes,simplified predictions are: (1) Green NDVI higher than 0.65 indicates 100% nitrogen nutrition state (N=100%); (2) Green NDVI lower than 0.25 indicates 0 % nitrogen (N=0%); (3) If Green NDVI value is in between 0.25 and 0.65, then nutrition state is calculated as N (%) = (green NDVI – 0.25) * 250. The nutrition state in younger plants during tillering should be generally higher than in later stages with emerged flag leaf.
  • Can N-Pen N 100 be calibrated to measure nitrogen values in other plants than barley, wheat and maize?
    Theoretically, the N-Pen can be calibrated for any plant species. In N-Pen leaf reflectance is correlated with nitrogen content that is determined by chemical analysis. Calibration procedure must include measuring optical signal with the N-Pen and analysis of chemically measured leaves for N content (standard AAS). Enough repetition is needed for statistical analysis; finding appropriate time and conditions for measurements during the plant growing season is also important.
  • What is the difference in between the LAI-2000 and LaiPen LP 100 ?
    LAI-2000 measures the attenuation of diffuse sky radiation at five zenith angles simultaneously, it has five detectors. The correct way of measurement is conditioned by attaching an appropriate view cup to hide foreign objects in the field of view. Our LaiPen is designed to avoid the system of view restrictor cups. This means it has a single view cup and a single detector and the four subsequent angles must be measured separately with the help of build-in electronic inclinometer and visual-acoustic indicator. In LaiPen, the permanent restricting cup has restriction angle 160 along x axis and 1120 along y axis, which is different from LICOR LAI 2000.
  • Can I correct measurements for clumping effects in the LaiPen LP 100 ?
    The only measurement you do with LaiPen is irradiance. In this respect, you can not correct measured irradiance values for clumping during measurement, but you can correct your calculation of LAI index afer you download irradiance values from LaiPen to computer.
  • What is the exact geometry/configuration of the ring sensors in the LaiPen LP 100 ?
    There are no ring sensors in LaiPen. Instead, the LaiPen device is equipped with a single wide-angle optical sensor used in conjunction with a cup restricting 160 / 1120 angle sector. All angles (in multiple angle measurement mode) are measured only with one sensor. The other four angles are obtained by subsequent inclinations of the device from zenith angle, which is controlled by electronic inclinometer with pre-defined five angle positions.
  • Can I exclude specific rings from the LaiPen LP 100 computation, or change path lengths of different rings (not homogeneous canopy) or measure single trees?
    In multiple-angle measurement mode you always measure all five angles. But since the data you download from the LaiPen to computer for further processing are only uncomputed raw values, exclusion of any measurement would be possible. It is not possible to change the path lengths - these are fixed. And the single trees measurement, for sure it can be done.
  • The website claims we can measure under different sky conditions with the LaiPen LP 100 , but the way the instrument deals with this is unclear?
    The dual sensor mode of measurement alows to estimate reference values for each particular time of measurement in changing weather conditions much more efficiently than the single sensor mode. The way how single sensor mode of measurement deals with this issue is decribed in the first version of Lai Pen manual (chapter 7.A. Single Sensor Mode of Measurement). The computation in case of dual sensor mode of measurement is described in the second attached file named: “Dual mode_ Introduction.pdf”, which is not included in the first version of manual.
  • Are you producing stand-alone infrared LED Light Panels (735-740 nm)?
    No, these panels are manufactured only as additional top LED panels for Close and Open version of the FluorCam instrument.
  • Do you place some filters in front of your LED Light Sources?
    No, LED panels are covered with clear glass as they are intended for illumination only. Filters are used for LED panels that are mounted in the FluorCam devices.
  • Light Controller LC 100 work without a PC?
    Yes, it is a stand-alone device.
  • Can PlanTherm PT 100 be connected to another display (than the provided one)?
    Yes, PlanTherm can be connected with every display with DVI connector; the device is supplied with the DVI cable (the white one).
  • What is calculation principle for PlanTherm PT 100?
    Both parameters, Ft as minimum chlorophyll fluorescence and conductivity changes, are measured by the appropriate sensors for obtaining changes in chlorophyll fluorescence and in conductivity curvature. Then the maximum inflexion points are evaluated using maximum of 2nd derivation and curvature.
  • In the PlanTherm PT 100, does the fluorescence excitation light source can be adjusted by ourselves?
    Yes, the intensity of the measuring flashes can be set in upper ribbon menu Settings/Ft. The inserted value should be 0-100 % of intensit;, 100 % intensity corresponds approximately to 0.09 µmol(photon).m-2.s-1 per pulse.
  • When we put the measured leaf into the liquid how long time it will be cost before activity of the sample is normal and can be measured in the PlanTherm PT 100?
    The leaf should stay in the deionized water as short time as possible, because of the leakage from the leaf. Is highly recommended to start measuring right after the leaf is inserted into the water.