MONITORING-PAM: FIELD OPERATING INSTRUCTIONS
Albert Porcar-Castell, Deparment of Forest Sciences, University of Helsinki.
joan.porcar@helsinki.fi +358405870444
Latest Update: 10.6.2010
1. BACKGROUND
The first step during the photosynthetic process is the absorption of light energy by chlorophyll molecules.
A variable fraction of this energy is re-emitted as chlorophyll fluorescence. The amount of energy reemitted as fluorescence depends, among others, on the current photosynthetic performance of the leaf.
Therefore, by monitoring and carefully analysing the chlorophyll fluorescence signal of the leaf we obtain
direct information on the diurnal and seasonal adjustments in photosynthesis.
2. MONITORING-PAM (Walz GmbH)
The monitoring PAM system consists of a number of fluorometers (up to 7) that are able to monitor the
chlorophyll fluorescence emitted from leaf samples in situ. The main components of the MONITORINGPAM system and the typical installation settings are:
SHELTERED (In cottage)
WEATHERPROOF (In tower)
220V/12V
AC/DC
Mains
<10m
<100m
USB Interface
MONI-DA:
Computer:
Alternatively if operated
in WinCotrol mode
Programable control
unit. Includes
battery and memory
card. Alternatively,
may be powered
with solar pannels.
MONI-heads: Up to 7
units. Leaves clipped in
the leaf holder. Records
PAR, Temp and
Fluorescence
3.MEASURING PRINCIPLE
The MONI-DA is programmed to trigger a measurement at a fixed frequency using its internal clock
(typically 5-30 minutes). When the measurement starts, the Moni-heads start emitting a blue modulated
light of very low intensity. This dim light induces a small modulated fluorescence signal (F’) that is recorded
by the MONI-DA. Subsequently, the MONI-heads emmit a pulse of supersaturating light which momentarily
saturates photosynthesis. Because no energy is then used in photosynthesis there is suddenly more energy
available for fluorescence and the fluorescence intensity increases until a maximal level (Fm). This level is
recorded by MONI-DA.
A posteriori, comparison of the F and Fm levels is used to estimate the quantum yield of photochemistry as
(Fm-F)/Fm. If the difference between F(with photochemistry) and Fm (Without photochemistry) is large it
reflects that photochemistry was indeed performing very well. Under optimal conditions the yield of
photochemistry is around 0.833. At the other extreme, if photochemistry is working very poorly, measuring
in the pressence or in the absence of photochemistry won’t make much of a difference and Fm won’t be
much higher than F, the result is that (Fm-F)/Fm (the quantum yield) will get close to zero.
Apart from estimating the photochemical yield, other slowly changing diurnal and seasonal parameters can
be estimated from fluorescence measurements. These parameters involve the comparison of fluorescence
levels from different points in time (e.g. morning vs. noon or summer vs. winter). Therefore, it is very
important the the same needles remain in the frame for the whole duration of the experiment, and that
the needles are moved as little as possible. Increasing, decreasing, or chaning the leaf sample will result in a
change in the absolute fluorescence level and needs to be corrected in post-processing. Always write down
in the diary if you need to re-insert, replace or move the needles in the frame, and never do it unless
necessary.
4. MEASUREMENTS IN HYYTIÄLÄ
The Monitoring-PAM system in Hyytiälä is installed following the diagram:
SMEAR-II COTTAGE
PHOTO TOWER
220V/12V
AC/DC
Mains
<10m
<100m
USB Interface
Computer: Computer
always ON and in
WinControl. Data save
through WinControl
MONI-DA
prototype: No
memory card.
Needs to be
operated through
WinControl. Battery
power.
MONI-heads: 4 units.
Leaves clipped in the
leaf holder. Records
PAR, Temp and
Fluorescence
5. MEASUREMENTS IN VÄRRIÖ
Four Moni-heads are installed in the top of the three Scots pine trees in the tower.
Tree 2
Tree 1
Tree 3
TOWER:
The Moni-heads have been installed in Tree 1 TOP, Tree 2 TOP, Tree 3 TOP, and Tree 2 MID canopy. (9 June
2010).
The MONI-DA rests in the tower. A 50m cable connects the MONI-DA with the USB-Interface in the cottage.
The USB interface is constantly connected to the mains so that the battery in the MONI-DA is always
charged (DISCONNECT IN CASE OF STORM). Data needs to be manually downloaded into a computer using
the MONI-DA MicroSD card.
The Moni-Diary is online. http://wiki.helsinki.fi/display/SMEAR/MONIPAM+%28Monitoring+PAM+Fluorometer%29+Diary Login to Wiki with your university account, press edit,
update the diary, save and exit. If it does not work, write in the hardcopy diary (it is under the USBInterface).
SMEAR-I COTTAGE
TOWER
220V/12V
AC/DC
Mains
<10m
<100m
USB Interface
MONI-DA:
Computer:
Alternatively when
operated in WinCotrol
mode. Data saved from
SD card
Micro
SDcard
Programable control
unit. Includes
battery and memory
card.
MONI-heads: 4 units.
Leaves clipped in the
leaf holder. Records
PAR, Temp and
Fluorescence
4.1 WEEKLY TASKS
1) Check that needles are in the frames and healthy. If not, reinsert and make a note in MONI-DIARY.
Needles should be replaced if they become yellow.
2) CAREFULLY Remove/blow away snow from the needles if applicable (See Winter Conditions). This can be
done e.g. with compressed air or carefully with the fingers, but not if temperature < -10C as the needes
may get damaged. Write down in MONI-DIARY if snow had to be blown away.
3) Check that MONI-DA is functioning properly. With the magnetic finger awake the system by moving it in
front of the ON button. The two LED lights should flash GREEN. If the MEM. light flashes RED there is no
memory car, the card is wrongly inserted, or it is damaged. If so, correct and if needed replace the memory
card. MEMORY CARDS ARE SUPER SENSITIVE!!! HANDLE IT WITH CARE AS DATA MIGHT BE LOST IF
DAMAGED!!
When the MONI-DA screen is active it should read:
MONI-DA (CFMH0114)
hh:mm:ss DD/MM/YY
Batch: mm:ss
M14-xxxx.PAM (file size)
/ The serial number of the instrument
/The time and date
/Batch: countdown to next measurement
/ File name and file size in kB.
Check that the time and date of the system are correct. Time is always Winter-time. If time is
not correct adjust accordingly:
From the main MONI-DA screen window, press MENU-> Date/Time-> Set the
new date and time and save. Write the changes in the MONY diary.
Check that countdown clock in Batch is running.If If it does not run:
disconnect from Computer if your are connected and wait for the batch to restart countdown. If it still does not run, do a RESET with the magnetic finger. If
that is no help, contact me (+358 405870444).
The last row shows the File name and size, file size should increase with each measurement
and a new file is created after each RESET.
4) Check that MONI-heads are functioning properly. The quality of the data can be reviewed in the MONIDA screen (or in the MoniBUS and Settings Window in WinControl). Go to the “Start window” in MONI-DA
(To make sure you are in the start window press ESC several times with the magnetic finger). Once there,
move the UP or DOWN arrows and you will see:
MONI-DA VALUES
I: +0.65A -0.08A // Shows the charge and consumption intensities, respectively.
If charge intensity is +0.00A the system is not properly connected to the
mains. Check the connections in the cottage. If battery in MONI-DA gets below
a treshold some MONI-heads might fail to deliber a pulse and the system will
eventually stops working. If charge is still +0.00A after checking connections
contact me. You will probably have to check that the internal fuse in the USB-
Interface is not broken. To do so, carefully unscrew the rear USB interface
and check fuse. Replace it if needed.
Ubatt: 12.4V (12.3 V). Denotes the Voltage of the internal battery, and (voltage during a
measurement). When properly connected to the mains Voltage is usually >13V. Voltage in
brakets should not normally get below 12V, if it does contact me.
Int: 18.2C 29% RH. Indicates system internal temperature and relative humidity
Next window is a TABLE with the results from the last measurement. It should show:
#: The number of the measuring head. There should be as many rows as Moni-heads are
measuring. Four?, if not, there might be some connection problem or MONI-DA battery
might be running low. Check connections as explained above.
Ft: The current fluorescence. This should be optimally >50. If Ft is smaller than 50 it may
indicate that needles are out of the frame, or there is snow. Correct if possible. YET if the
measuring light is not swithced ON. F will appear as a negative value, that’s normal.
PAR: Incident PPFD.
Y(II): the quantum yield of photochemistry (This value ranges from 0.83 during summer
nights to <0.05 during cold winter days).
Once everything is ckecked leave the magnetic finger in its place, check once again that the clock is still
running and that’s it. Alternatively, Steps 3) and 4) can be checked through WinControl, but better to do it
in MONI-DA. (WinControl instruction will come later)
4) Download the data.
Take the microSD-USB adapter to the tower (it is hanging in the cottage by the MONI-PAM Interface-box).
Open the black screw from the rear of the MONI-DA with your fingers. Push gently the micro-SD card you
will find under the screw so that it gets free and take insert it into the microSD-USB adapter. Place the
screw back in place as humidity might get into the instrument. Take the USB adapter to the cottage and
download data into Lenovo Laptop (C:\Desktop\MoniPAM Data), password is “monipam”. Alternatively
into another computer if the Lenovo is not available. If the computer asks to Fix or Correct the SdCard
don’t let it do it, it might erase the data. Once copied, take the micro-SD card (inside the USB-adapter) back
to the tower and into the MONI-DA slot. Screw well. If the card is near to full you can empty the card after
copying the data, however 1GB should suffice for several years of data!!
When using a new card, format it first in MONI-DA, after inserting the new card go to MENU
->Data tools ->Format Card-> YES. The system is then reset and measurements started using
the new card.
Plan B) If there is no computer: Take the spare microSD card (next to the USB-interface in the Cottage).
Replace the card from the MONI-DA (with the data) with this one and press RESET. Download the data into
the Värriö Library computer as described above (Make a new Folder, e.g. MONIPAM). Once all the card
contents are copied into the computer empty the card and store it in its place in the cottage. Keep swaping
cards each week.
5) Send the data weekly to: joan.porcar@helsinki.fi and benat.olascoagagracia@helsinki.fi
6) Artificial darkening (during summer). Reference night measurements are needed to calculate some
parameters. For the period when there is no proper night, e.g. PPFD>5 the whole day. The Moni-heads
should be darkenned for 2 hours at least once a week (better twice). To do so, place the covers VERY
CAREFULLY (needles may move or get out of the frames otherwise) onto the Moni-heads and leave them
for 2 hours. If possible, select cloudy days to do the darkening. If the covers are damaged you can make
new ones with the aluminum paper, please fill free to improve them as I made them in a hurry.
ANNUAL TASKS:
1) Special cylinders (transparent) for winter measurements under the snow. These should be placed
either before the tykkylumi appears or when there is no longer daylight, and removed as soon as the
tykkylumi is gone. COMMING SOON !
2) Winter/Summer batch. The batch file is a small program that controls the frequency of the
measurments. Frequency is kept as low as possible to minimize the secondary effects on the needles.
SUMMER (c. 15 May- 15 Aug)
WINTER (c. 15 Aug- 15 May)
Normal Frequency
20 minutes
30 minutes
Night Frequency/ PAR<3
30 minutes
120 minutes
1 day out of 7
10 minutes
15 minutes
Summer is the period when there is no proper night.
To change the batch files between SUMMER and WINTER, connect the USB-cable from the
USB-Interface to the Lenovo Laptop. Open WinControl. Click on “View” (top left) and select
“batch window”. Click on the Open icon. Select the required batch file from
C:\DESKTOP\Batch Files. When the new batch file appears in the screen, select the button
“MDA Compat.” and Press “Send to MDA”. The new batch file is now in use by MONI-DA.
Close WinControl and disconnect the USB cable. Check the MONI-DA in the tower, is the
batch clock in countdown? The batch file starts from the 1-day-out-of-7 frequency (i.e. 10
minutes for the SUMMER batch, and 15 minutes for the WINTER batch), Is the new
frequency already in use by the MONI-DA? if so, that’s it!
3) Change the Micro SD card(s) every year during early June. Micro SD cards should last for several years
but since they are relatively cheap its better to replace them regularly.
If you have any questions or there is any other problem you can contact me by phone or e-mail. If needed
the MONI-DA User’s manual can be found in the desktop (C:\Desktop\Manuals).
Albert Porcar-Castell
joan.porcar@helsinki.fi +358405870444