MITESS profiler Instructions Version 2.8 updated June 5, 2003
1. MOORED SAMPLER COMMUNICATION
2. MOUNTING BOTTLES IN BOTTLE HOLDERS
3. ASSEMBLING THE MOORING UNIT
6. REPAIR AND REASSEMBLY OF MODULES
7. MODULE HANDLING: GENERAL TIPS
8. MITESS PROFILE 500 ml BOTTLE PREPARATION
(see attached picture files as well)
1. COMMUNICATION: OVERVIEW
The IR wand attaches to the serial port of a Macintosh using a standard DIN-8 cable. (Be
sure that Appletalk is not operating on the port). The hole on the black plastic triangle fits onto
the bottom locking piece of the bellows. When it is pushed all of the way down, it will be in
exactly the correct position. Keep the wand dry, especially avoiding salt water which may short
out the wand.
On a Macintosh, use the “Zterm” telecommunication software “PT 100” on a Newton, or
“Terminal” or “Hyperterminal” in Windows. (other programs may work too, but some programs
assume or require handshaking which prevents the wand from working properly). The
communications program should be set to 300 baud, 8-N-1 (8 bits, no parity, 1 stop bit), and NO
handshaking or flow control. You should type slowly, or set the inter-character delay on the
communications program to something large enough to work reliably (60 works; you might try
slightly lower settings).
The Excel spreadsheets "Now Hex / Timing" and "CTD calculations", and the "log parsers"
for the time calculations use "macros", so make sure they are installed on the excel add-ins
menu (Analysis Toolpak in the most recent versions). Specifically, hex2dec and dec2hex
functions are required.
Program the units under low light levels. Sunlight or bright indoor lights can interfere with
the programming. If you have difficulties programming, try covering the unit with a dark cover.
Note that with some units the programming and timing commands sometime fail to “stick” and
you may have to try multiple times.
Sampler IR Commands:
r report (current clock time, time programmed to open, number of flags (00
after reset), number of resets, time to hold bottle open,
time of last low battery condition (all in hexadecimal form).
l log (reports times for start open, fully open, start close, fully closed)
y program mode enable ("yes") (4 of these in a row lets you use the programming
o manual open (for bottle loading)
c manual close (for bottle loading)
s stops the motor from a manual open or close command
t program the current time (8 characters in hexadecimal; no spaces)
p program the open time and duration open (10 characters; first 8 are time,
last two are full open duration)
u plus time (increment time up by 1)
d minus time (decrement time down by 1)
k soft-reset ("klear")(resets the flags, and gets the unit ready for a new program)
n program mode disable ("no")(when used in program mode, drops unit back to
Commands r,l,s, and y work at any time.
All other commands require four consecutive 'y' commands to put the unit into program
mode (to avoid stray light commands). To get out of program mode, you send a single 'n' (more
'n's will just be ignored... which is generally the case with non-command characters).
At various times, the unit may report text saying "pmc 0#" where that number is between
00 and 04. This is the program mode counter (counting consecutive y's). When it is 04, you are
in program mode... anything else means that you are in protected mode. The value will usually
be either 0 or 4, unless you are typing y's in order to enter program mode.
The current time and the program open time are 4 byte (8 character) values, representing
a time standard (the time from the beginning of 1904) in 8 second intervals (so 00 00 00 01 is 8
seconds). The time to remain open (wait) is a 1 byte (2 character) value of the same metric.
The reset number given in the report reports the number of resets
(usually caused by loss of power) since the last time the program was
cleared (see 'k' command below).
The log information gives data on when events actually happened; this data is saved in
eeprom ("electrically eraseable and programmable memory". This memory is non-volatile; in
principle, even if power is lost or the board ceases to function, the data can be read by
connecting the microprocessor to a working board). The four values are the time the bottle
started opening, the time it stopped opening, the time it started closing, and the time it finished
To program the current time (i.e. the clock), go into program mode and type 't'. Then type
the 4 byte (8 character) hex representing the Macintosh 1904-based date-time in 8 second
chunks (attached spreadsheet "NowHex/timing" from should make this calculation clear). Note
that the hexadecimal macro calculations do not update automatically; you have to press "=" to
update the time. To enter the time from the spreadsheet into the unit, copy (-C) the time cell and
paste (-V) into Zterm (set the character time to ~3 (0.05 sec per character): Settings:Text Pacing
- character delay, in 60ths of a second. If the current time on the board is not quite right, you
can use the 'u' and 'd' commands to tweak it by 1 unit. Each time you issue these, you will get a
"report" indicating the new time.
To set the sampling time and the bottle open time, go into program mode and type a 'p'
Then type the 4 byte (8 character) hexadecimal representation of the 1904 date-time in 8 second
chunks, followed immediately by the 1 byte (2 character) number of 8 seconds you want the
bottle to remain open ("wait").
While in program mode, type 'k' to clear the flags. THIS STEP IS EXTREMELY
IMPORTANT; IT ALLOWS A NEW SAMPLE TO BE TAKEN. OTHERWISE, THE BOARD WILL
NOT COLLECT A NEW SAMPLE. [The lower nibble of the flags indicates bottle started opening,
bottle finished opening, bottle started closing, and bottle finished closing. 0 means it is ready to
collect a sample). Only 1 bit of the upper flag nibble is normally used; it indicates whether the
batteries are low (1 indicates they are low; the batt: line in the report will tell you when the battery
was recorded as being low. In this context, low is between 5-6V compared to 9V when fresh). If
the upper nibble is anything other than 1 or 0, then an error occurred, and you should record the
error code and all report/log information; the sample is probably not valid. Battery low condition
records the time a low battery has been encountered; it is never reset until the board encounters
a new low battery condition. So it is possible for a past low battery condition to be confused with
a more recent cast. The low battery condition is only a cause for concern if it changes during
your deployment, and if the time indicated is a valid time possible since you set the clock to
After the bottle opens and closes. it will try to tighten the bottle a bit (3 pulses a few
seconds apart. This is normal.
2. MOUNTING BOTTLES IN BOTTLE HOLDERS
Adjust the tightness of the bottle cap on the bottle so that it is just sufficient to seal the
bottle. If the cap is too tight, the bottle will not open! Because the bottles are shipped with a
very tight cap seal, you must check each bottle before mounting to ensure that the cap is not too
tight. [If they are too tightly closed and the bottle can slide in the holder, the bottles could remain closed as the
holder slides out from beneath]
The bottles need to fit tightly into the cups. Differences in cup and bottle sizes may require
modifications to this procedure, which is given as a default for bottles which are loose in the
cups. If the bottles fit reasonably snugly, you don’t need to do this! Tightly wrap the bottom of
the bottle with a thin layer of parafilm (~8" of 2"-wide parafilm), then ~15” of Duraseal
polyethylene film (4" wide, folded in half to 12"x2"), then another thin layer of parafilm (as
above) (Figure 1). [These are added to ensure a tight grip on the bottle. Practice this a few times to make sure
that you are getting a good seal. If the seal is too loose, the bottle slips and will not open.].
Wrap a stretched parafilm seal (about 6” x 1/2” initially) around the side edge of the cap to
keep the bottle cap securely in the cap holder. Make sure that the parafilm is tight and does not
come loose during opening (and get caught in the bottle). Using a black Sharpie, place a mark
on the bottle of the body on the seam and immediately above on the top of the cap (not on the
parafilm). This alignment will shift towards the “extra cap twist” direction if the unit works
properly. Give each sample bottle a number with a black sharpie pen corresponding to the
station, cast and body of the sampler it will be in (e.g. Sta 1, cast 1, unit E2). Put this number on
the side and on the bottom of the bottle also (in the depressed portion that will not rub up against
When the bottles are in place, force sawed-off (1000 µl) pipet tips (figure 2) into the cup
holder at three symmetrical positions (figure 3). The distortion of the bottle will make for a tighter
grip of the bottle by the cup holder. The pipet tips are cut off about 1/4 inch above the
conical/cylindrical transition level (figure 2).
Communicate with the unit using the computer/wand. Using the “o”, “c”, and “s”
commands, move the bottle so that the bottom of the cap aligns with the top of the thick part of
the rods (figure 4). Then place the cap holder on the cap (grip side down)(figure 5). Be sure the
cap is tightly gripped so that it does not fall out when the bottle is open
3. ASSEMBLING THE MOORING UNIT
This task is best done with two people - at least at certain critical times. Also, be careful
because many of the mooring parts are heavy, get stuck and offer ample opportunity for
smashing fingers and toes. The task is awkward at points (please understand that this was done
to make it extremely unlikely to come apart on a mooring, at the cost of slightly difficult
The moored unit consists of:
1 plastic-coated 1" stainless steel rod with flat welded mounting pins and bottom metal plate
2 bottom plastic plates
1 top plastic plate
6 long plastic strength rods
6 plastic mounting nuts.
The bottom plate (with the hex holes on the bottom side) slides over the bottom
attachment pin; the other slides down the rod from the top; the metal plate is held within a groove
within the bottom of the upper-bottom plate. Put these plates on first.
Place the mooring unit vertically (figure 6), either by placing on a stand with a hole or by
having someone else hold the unit up. Put the sample modules together in groups of three (half-
hexagons) (figure 7). Assemble the first and second groups into a hexagon surrounding the rod
with the feet fitting into the holes figure 8). When a layer is complete, wrap a bungy cord around
it to hold it together (figure 9). Put the second two groups together on top with the feet fitting onto
the top knobs of the bottom hexagon (and secure with a bungy cord) (figures 10, 11, 12). Put the
top plate on, pushing or pounding it down until the top knobs of the top row fit into the holes on
the underside of the plate (figures 13, 14). At this point, the welded top pin should be capable of
freely rotating. If it is not, the bottom feet of the bottom row of samplers are probably not pushed
down into the holes in the lower (middle) plate.
Rotate the metal plate to right angles with the top slot (figure 16), so that the 6 long
mooring holder rods can be inserted through the bottom, thread end coming out of the top (this
configuration ensures that the sampler will not dissassemble itself). Put the unit on its side, make sure the
bottom plate is in position. You might have to rotate the bottom plate at this point to get it in the
right position (figures 18, 19, 20). Insert the rods (figures 21, 22). Then place the unit vertically
(figure 23) and screw on the nuts (figure 24) (a little silicone grease may make this easier, and a ratchet
hex wrench w wooden bloack holder can make tight fits easier, figure 25). After they are secure, the nuts are
linked together with cable ties to keep them from unscrewing (figure 26).
Note that the slit in the top of the unit is close to the inlets to the top row of bottles. To
eliminate the possible flushing of iron from the top of the unit traveling down into the sampling
layer, stuff the slit with parafilm to make a tight seal.
Too much light activates the IR communication ports and draws battery power. So to
prevent this from happening, cover the externally-facing IR ports with a small piece of electrical
tape and cover the samplers with dark garbage bags when they are not being used (this also
helps keep them clean).
When everything is set, secure the unit and cover it with plastic bags (one garbage bag on
top, another turned into a tube by opening the bottom on the lower half) to keep it clean until it is
MITESS should be deployed with a swivel above it to avoid accumulated twisting
(otherwise, it may untwist rapidly as it is raised above the surface).
Program the units according to the “CTD” calculations spreadsheet: you copy and paste
the appropriate cell from column “K” (copy to Zterm). Read the “report” and verify that the
program time and open time are correct. This step can be done anytime before the cast.
JUST BEFORE THE CAST: set the clocks. You should set a timer to zero (noting the
true time so that you have a safety backup) and then immediately begin setting the clocks.
Typically, programming 12 modules will take about 20 minutes, but adequate spare time should
be built into the schedule to allow for problems. Use the “Hex Time Table” to convert from
minutes:seconds to hexadecimal. Then, to set the time, you type in “t000000” and the two-
character value from the hex time table. Allow one second between digits if you type manually.
Then type “r” to verify that the time has been properly set (and that the program has not been
inadvertently altered). Some units are difficult to set; you must be patient and keep repeating this
step until the time is right.
Sometimes a communications error will result in the program being reset (this is particularly a problem for
those “difficult to set” units). When this happens, you must then reprogram the unit before setting the time. Keep a
copy of the programs handy so you can do this without losing time.
When the clocks are set, get the unit into the water and down to the first sample depth as
soon as possible.
Direct the winch to stop at the right depths at the right time. Use the timer started in the
previous step to A sample sequence consists of the following steps: the unit should arrive at the
correct depth one “arrival safety time” (typically one minute) before the sampler starts to open.
Then, it takes 2-3 minutes for the sample to open, and then it stays open for the programmed
“bottle open time” (typically 7 minutes). The sampler then takes 2-3 minutes to close. An
additional “close safety time” (typically one minute) pause is allowed. Then, the winch should
start moving down at the “winch speed” (up to 50 meters per minute) until it reaches the next
Sometimes a winch problem or operator error will result in a misstep, and you have to “scramble” to recover.
Here are some things to consider when this happens: (a) if the misstep is only a couple of minutes, you can use the
arrival safety time and the fact that it takes some time for the bottle to fully open to recover, (b) If the error is larger,
then consider changing the sampling depths to coincide with what is now possible. A sample could be skipped, or
you can just collect samples at different depths than you originally intended. BUT DON’T FORGET THAT THE
OPEN TIMES ARE NOT CHANGING; you must arrange to be stopped at an appropriate depth when the samplers
Before you disassemble the modules, check to make sure that the number marked on
each bottle corresponds to the number of the module body. Note any abnormalities: bottles not
closed, crushed, whatever, and record the state of the unit with respect to fouling.
Interrogate each module before you remove the bottles. Open Z-term, turn on the capture
mode (so the data is saved to hard disk as you read it). Note the present time per the usual
standards and then immediately "r"eport to get the module time. "l"og to get the opening and
closing log. Note any units that fail to respond. If the reason for their failure is low batteries, the
"r" low battery and and "l" log information is preserved and can be recovered by replacing the
batteries. Try this first, then note any that fail to respond entirely. It is possible that the
information is still on the PIC chip, and putting it on another board may allow us to recover it; this
attempt should be done at MIT rather than in the field. Keep a record of the real time that each
unit is interrogated, so that the accuracy of the clock can be assessed. This is most easily done
by reading all samplers rapidly in sequence, noting the beginning and end times and
interpolating in-between. Then turn the capture mode off.
As you remove the bottles from the module bodies, verify again that the bottle numbers
match the module body numbers. Check to make sure the bottles are tightly sealed (if the unit
has operated properly, they should be tightly sealed; make a note of any that seem a bit loose).
Record whether or not the cap positions have been twisted past the mark (verifying
After the bottles are removed, make sure the caps are sealed tightly, then put them in
plastic bags (keeping in mind that some of them might have 1N acid if they have not fired
6. REPAIR AND DISASSEMBLY OF MODULES
A unit that has worked and doesn’t indicate a recent low battery indication can simply be
re-used after putting a new bottle into the holder.
If there has been a problem with the battery or electronics, you have two choices:
disassembled the unit and put it back as an empty body (for MITESS mooring holder structural
integrity), or take the unit apart, clean it up, and replace the batteries and/or boardmotor unit.
Before you disassemble the unit, open the bellows knob and pour the fluorinert out into a
sealed bottle. After you open the unit, additional fluorinert can be poured out of the battery
compartment. Remember, fluorinert is volatile and expensive!
Leaking or exhausted batteries should be removed and discarded.
The bodies should be completely dried before being reassembled. If salt water leakage is
evident, you should rinse the unit with fresh water and dry thoroughly. This step is particularly
important for the bellows unit, which can trap small droplets of water. Use a Q-tip to dry out the
bellows, and keep repeating until the Q-tip comes out dry.
PREPARING FOR RE-USE:
If you replace batteries or boardmotors:
Replace all of the o-rings on the modules (bellows gasket, bellows cap, motor shaft).
Lubricate them with a liberal film of silicone grease. Place the battery packs inside of the main
body and partially insert the boardmotors. Solder the battery packs onto the board, being
extremely careful not to damage the body with the soldering iron. Put the thin polyethylene foam
circles on top of the batteries to prevent shorts to the board. Then insert the boardmotors into the
unit leaving a slight space for fluorinert to penetrate into the battery compartment. Add fluorinert
to the main body until it nears the top. Gently push the boardmotor into its fully inserted position.
Put the bellows unit on and tighten into place. Pour fluorinert into the bellows, rapping the
sides to eliminate bubbles. Add fluorinert until you reach the top of the cap hole. Pull the bellows
upward until the fluorinert reaches the bottom of the caphole, and screw in the cap (tightly, but
not too tightly). On some units with thick caps, too much fluorinert might prevent assembly of the
mooring holder; you will have to relieve some of the excess pressure if this happens.
7. MOORED SAMPLER MODULE HANDLING: GENERAL TIPS
Only use fresh Duracell alkaline C-cells. Sony cells are OK as a
last resort. For deployments at >200 m depth, the cells need to be drilled to allow fluorinert
pressure compensation (see separate description of battery drilling process). For deployments
below 0°C, you should use special lithium batteries.
Replace the o-rings on the bellows, bellows cap, and motor shaft with new o-rings on
each deployment. The o-rings seal much better if they have a liberal layer of silicone grease.
[Actually, these are "quad-rings", not o-rings. Note that quad-rings have a preferred orientation,
which is what you find them in before you use them. You should make sure that these are not
twisted against their natural orientation.]
Alternate polarities when loading the batteries. While looking down at the sampler
body when loading the batteries, start with the positive side up for the battery counterclockwise
to the IR component holes. If you are using welded battery packs, this alternation should be fixed
Solder the wire from the board onto the battery pack clips. Be sure to bend the
battery interconnection tabs so that that they contact the bottom of the grooves between
the batteries. Remember to place the plastic foam coverings on the top of each battery.
(These steps are taken to prevent shorting the board.)
When seating the board/motor assembly in the bodies, be careful about the IR
components around the edge of the board and make sure that they are placed into the
correct position as the board is inserted (it helps if they are bent outwards slightly). They can
get bent in shipping, and then get squished when you put them in. If this happens, the IR may
not not work properly, and the bellows sealing is endangered.
Filling the sampler with fluorinert: After the batteries and board/motor assemblies are
mounted (but before putting the bellows on), pour fluorinert into the battery compartment until
just up to the level on the board. Immediately afterwards, put the bellows on. Fill the bellows
chamber. After filling, tilt it to one side and then another for a little while to let bubbles come out
of holes near the center of the board. This helps get rid of air in the sampler. You can also use
the heel of your hand to knock on the samplers while tilting and rotating. Before sealing the
chamber with the cap, pull up on the bellows a bit and fill to the top with fluorinert. This provides
a bit of excess pressure to help avoid seawater leaking in. However, note that for some mooring
holder/cap combinations, too much filling may prevent you from putting the mooring holder
together. If this problem occurs, you will need to bleed a little fluorinert out of the bellows.
Fluorinert is very expensive and should not be wasted. We recover all used fluorinert
and recycle it (either by simple repeated washing with distilled water in a separatory funnel
followed by drying over white Drierite, or if necessary, distillation using refrigerated water on the
condenser). Use a funnel or a small poly bottle to put the fluorinert in; use a funnel to empty the
To load a bottle, put the closed bottle (ie with cap) in the unit bottle holder (with the top
piece off). Then use the software (see instructions below) to rotate the bottle up until the bottle
cap is where you want it. Then put the cap holder on, by just spreading the rods till the balls lock
8. MITESS CAST 500 ml BOTTLE PREPARATION
See notes in lab books 24-109 and 24-150 for evolution of process.
1. 500 ml linear polyethylene bottles are cold-acid leached in 1N HCl in a vat where the caps and
threads can be leached. (Note: polyethylene bottles contaminate for aluminum. If you want to get good
aluminum data, you must use teflon or PMP bottles, which require a different pre-cleaning treatment).
2. The bottles are then filled with 1N HCl and acid-leached for 24 hours at 60°C. The bottles are
then turned over and allowed to sit for one more day.
3. The acid is poured out (into other bottles awaiting leaching) and the bottles are filled rinsed
three times with high purity water and then filled with high purity water to the top. 100 µl of
high-purity 6N is added to the bottle and then it is capped until use. And don’t forget, just
before putting bottles into modules:
4. Make sure the caps are not too tight!
5. Wrap a thin highly stretched parafilm seal around the edge cap (this helps the cap holder grip
the cap when the bottle is opened). Place a pinhole in the parafilm to allow for pressure