Oil testing kit Beta programme - Assembly: spectrometer

by cindy_excites | over 8 years ago | 0 | 0

Oil testing kit Beta programme - Assembly notes Part 3: spectrometer

Contributors: @TedF and @cindy_excites

Date: 31/Oct/2015

Here we document our experience assembling the spectrometer frame and put forth a few humble suggestions.

1) Bench assembly Following the instructions on how to build the Desktop spectrometer Kit 3.0, we started by taping the 'loop tape' to the 'ash bench'. The instructions feature an image with a narrower version of the tape:

This is the new wider tape that came with the kit:

NOTE: To apply the loop tape, we placed the tape near the edge of the ash board and the slowly peeled-off the protective tape layer, allowing for an easy way to guide the tape onto the board (which would otherwise be difficult to remove in case the tape is laid down crocked). We also cut away the overhanging bit of loop tape:

2) Camera block assembly

i) Here we reverse the steps by attached the 'hook tape' to the block first:

NOTE: Being a bit wider than 2cm, the two pieces of hook tape overlap slightly in the middle.

ii) We then prepare the camera for mounting:

NOTE: We adhere two sides of double-sided tape. Rationale: one tape down the middle might cause the camera to wobble from side to side; two tapes provide stability.

iii) We attach the camera to the block ensuring that the camera's board is flush with the base of the block (otherwise the height of the camera might be blocked by the top part of the 'mid-point' hole of the 'diffraction grating angle' (see construction of this part below)).

3) Making a diffraction grating from a DVD

The instructions of this are very good. Very smart to start with "Do not touch the surface of the DVD" ;).

As note in our calibration research note, we had qualms about the DVD fragment's quality due to unsatisfactory separation. If the quality of the DVD fragment turns out to be problematic, I'll try @ethanbass's recommendation with MrBumper's method ).

Our qualms was due to our DVD not having been peeled/separated properly (even after several tries, the DVD that came with the kit was rendered unusable so I used one from an unopened DIY foldable paper spectrometer, which proved to be more resilient):

Does it matter if it still refracts the light? What is good enough for a DVD fragment? Here is our piece of DVD:

4) Assembling the diffraction grating angle

Upon seeing the design, I wondered what inspired it. Maybe a direct link to a development research note on this would be nice for the incurably curios ;).

i) We used two strips of double-sided tape when taping the three flaps together.

Conveniently, the hook tape fits perfectly on the base of the diffraction grating angle.

ii) We place the DVD fragment on top of the mid-point hole in the diffraction grating'. We have to admit that since we did not understand why the DVD fragment didn't have to cover the whole of the 'mid hole' of the 'diffraction grating angle' I covered the whole thing. (Might be good to add info to answer 'why is the outer edge of the DVD used' and 'why is one half the mid-point hole covered'?) And we remove the handles from the binder clip:

5) Assembling the slit card

Also great instructions for this. We aligned the collimation slit with the line on the slit card as best we could:

The design for sliding the collimation slit card is brilliant!

6) Assembling the box

The assembly video is excellent! And very well complemented by the photo-based walk-through.

We only had two little hiccups.

The first was that one of the folds was not pre-marked. To facilitate the folding of this flap we slightly ran a cutter along the cardboard using a ruler:

The second hiccup was making the mistake of not carefully reading "Make sure the small rectangular holes on the top and bottom of the box line up. We will put the webcam cable through that hole later." And also missing the concomitant photo that states "Align holes here"…

So we document our 'error discovery' here:

7) Final steps

i) A little note on leaving a gap between the edge of the ash bench and the camera block might be good to add, rationalising the space needed for the smartly suggested knot on the cable.

ii) Inserting the bench and connecting the camera's cable:

And the left over screw this time is…

(Where does this go??)

This was a very satisfying assembly process. It is very enjoyable to go along with Aha! moments at every step realising the rationale behind the intricate design! Thank you for this!

Other research notes in this series:

Oil testing kit Beta programme - Package content

Oil testing kit Beta programme - Assembly: cuvette frame

Oil testing kit Beta programme - Calibration

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Oil testing kit: Testing

by ethanbass | over 8 years ago | 10 | 7

What I want to do

I wanted to see if I could use the oil testing kit to fulfill its goal of reliably distinguishing between different grades of oil.

My attempt and results

When my spectrometer is placed flat on the table facing the opening of the oil testing kit, the alignment does not produce a reading. My first, quick and dirty solution was to wedge a pipette under the front of the spectrometer to adjust the angle of its interface with the cuvette holder. I used this method for all of the data I gathered on October 23rd, but I became concerned that the instability of the angle was adversely impacting my results. After some experimentation, I designed a simple platform for the spectrometer, made out of paper, which succeeded in improving the alignment. I determined the proper height for the stand based on trial and error. Yagiz has just pointed out to me a different solution to this problem.

spectrometer propped up on paper platform to improve slit alignment

A. Documenting known samples:

(https://spectralworkbench.org/sets/2672), crude oil spectra

(https://spectralworkbench.org/sets/2673), diesel oil spectra

(https://spectralworkbench.org/sets/2685), a direct comparison between diesel and crude highlights the differences between their fluorescence profiles. Diesel has one large peak at 475 nm whereas crude has a much broader distribution, with several peaks spread out from 480-530 nm and an additional red peak at 580-590 nm.

This is a figure from Hengstermann and Reuter, 1990, comparing emission spectra from diesel and crude oil. I was excited to see that the shapes of the spectra are a good match for my results! According to the LIF literature, it is to be expected that the wavelengths of the fluorescence emission spectrum will vary according to the wavelength of the excitation source that is used (in this case, our excitation source is a 405 nm blue-ray laser). However, we see here that the shapes of the fluorescence emission spectra are consistent with the results published in the literature.

The additional red peak of the crude oil (bottom) pops out even more in RGB mode.

(https://spectralworkbench.org/sets/2674), 80w-90 spectra on the top with RGB mode on the bottom

(https://spectralworkbench.org/sets/2686), comparison of 80w-90 with crude oil. The distributions here are much closer. The biggest difference I see is the strong red peak for crude oil at ~580 nm which does not show up as strongly in the 80w-90 spectra.

(https://spectralworkbench.org/sets/2676), spectra for 20w-50

(https://spectralworkbench.org/sets/2689), comparison of 20w-50 and 80w-90 -- 80w-90 appears to have a broader distribution with more emissions from 500-550 nm whereas 20w-50 has most of its emissions from 470-515 nm.

(https://spectralworkbench.org/sets/2675), 5w-30 had by far the weakest signal, resulting in this squashed looking graph when I tried to use area equalization.

The height equalization macro yielded a much better looking graph for 5w-30. I'm still a bit suspicious of this data because of the weak signal. I plan to test some dilutions of the sample to see if the signal strength can be improved.

B. Investigating unknown samples:

All of the unknowns gave me fairly weak fluorescence compared to the rest of the oil samples (though not as weak as 5w-20).

(https://spectralworkbench.org/sets/2679), unknown 25

(https://spectralworkbench.org/sets/2678), unknown 29

(https://spectralworkbench.org/sets/2680), unknown 93

The fluorescence emission profile of unknown 25 matches most closely with 20w-50

The emission profile of unknown 29 is slightly to the left of unknown 25. It falls between the spectra of 20w-50 and diesel fuel.

Unknown 93 shows good segregation with 80w-90.

Also, here (the green line is 80w-90 and the three lines clustered around it are the 3 captures of unknown 93).

Questions and next steps

I want to test dilutions of the samples to see if some of the spectra can be improved by making dilutions and, most importantly, whether the shapes of the spectra stay consistent for each sample when they are diluted.

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Oil testing Kit: Collection of Samples from Pavement, Boqueron Puerto Rico

by ernestootero | over 8 years ago | 7 | 4

Collection of Unknown Samples I decided to test paved areas showing residues from cars. I did that in areas near a coastal town of Boquerón, PR. 4 samples were collected, one of them a blank from pavement that did not show traces of oil. See Map.

I used Q-tips and a small amount of mineral oil (MO) for human consumption (no additives on the label). I added ca. 1mL of the MO to the residues on the pavement and recovered as much as possible of it swabbing the Q-tip and squeezing the cotton on the inner surface of the vial.

Different levels of color were recovered and basically none in the pavement blank. Mineral oil was added to all samples to achieve a similar volume.

SINCE FLUOROMETRY IS VERY SENSITIVE TO TURBIDITY AND PARTICLES, I WILL WAIT FOR A FEW DAYS BEFORE ANALYSIS. IF IT DOES NOT WORK, THEN SOME SORT OF SIMPLE FILTRATION/CENTRIFUGACION METHODS MIGHT BE NEEDED. THE ADDITION OF DEHYDRATING SALTS TO REMOVE WATER FROM SOLUTION AND DECREASE TURBIDITY.

LETS SEE!

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Oil testing kit: Assembly + Initial Calibration

by ethanbass | over 8 years ago | 5 | 3

Hi, I'm Ethan, a member of the Oil Testing Kit beta program, located in Chicago. Here I've collected some notes and pictures from the assembly and calibration of my oil testing kit.

Unboxing:

Unloading the oil testing kit

Oil testing kit contents: oil samples, cuvettes, eyedroppers, pipettes, etc.

Contents of the spectrometer v3.0 kit (my card-stock was a little warped coming out of the box but it wasn't too problematic)

Assembly:

Preparation of the DVD diffraction grating:

I cut the DVD that came included with the kit into quarters, but unfortunately none of my fragments split apart cleanly.

Instead, almost all of the aluminum stuck to the bottom of the disk, so these pieces were useless as a diffraction grating.

I am experimenting with MrBumper's method of loosening the aluminum layer in a lye bath.

In the meantime, I found an old, scratched-up DVD that split apart cleanly

Spectrometer housing:

• The assembly of the spectrometer's housing went fairly smoothly after I consulted the materials on the website, but the reproductions in the booklet were very hard to make out.
• In spite of the warning included in the instructional booklet, I initially folded the top of the box with the inside facing out, so that the cable holes were misaligned.
• This hazard could be avoided if the top of the box were printed with a pattern to differentiate between the inner and outer surfaces.

Desktop Spectrometer v3.0

Velcro bench, block and camera:

My assembled camera block

Assembly of the diffraction grating angle (I opted for extra tape)

• The velcro bench system is clever because it's sturdy enough and you can adjust it easily, or add new parts to the spectrometer, if necessary.
• I had a lot of trouble getting the camera to stay mounted. Even after doubling up the tape on the back of the camera, I found that torque from the camera's USB cable is strong enough to easily dislodge the PCB, if the spectrometer is not handled extremely carefully.
• Has anyone used the mounting holes in the PCB to screw down the camera? I think this would help a lot to stabilize the camera and improve replicability of the results.
• Why isn't the face of the camera block cut so that it supports the entire length of the PCB? Are the mounting blocks cut at Public Lab or are they a pre-fabricated part? I couldn't help thinking that having full contact over the entire length of the camera would provide a lot more stability, even using just the sticky tape. It would also open up the possibility of using the PCB's 3rd mounting hole, next to the micro-USB port.
• Another thought I had was that it might be possible to reduce torque on the camera by fastening the USB cable to the back of the mounting block.

Cuvette frame assembly:

When I laid out all of the pieces, I didn't know what the function of each part was meant to be or how they should fit together

• It would have been helpful to have a diagram with a short explanation of each piece, so that it would be obvious which piece is the cuvette holder, which piece is the laser attenuator and so on. Or the parts could have labels printed on them.
• It was difficult to interpret the documentation because the edges of the black card-stock are very difficult to make out in the pictures (even more so in the reproductions included with the kit).
• It would be useful to have diagrams with arrows illustrating the directionality of the folds, and/or a video.

This was probably the easiest fold, but it took me a few minutes to figure it out, even though it's obvious once you see how it's meant to go!

The proper method of folding the cuvette platform took me an extremely long time to figure out. My paper-folding skills are definitely not up to snuff, but better documentation would help.

• I had to notch the smaller triangular holes with a razor blade to get the laser holder to push through the middle of the “M-folded sheet.” I spent a while trying to force the "V-folded sheet" through the holes before resorting to the razor blade, resulting in some slight crumpling along the edges of the laser holder. I see that some other beta testers had the same idea.
• To my mind the smaller triangles also do not allow enough clearance for the laser to slide in and out of position easily enough.
• I also found it useful to notch the edges of the laser attenuator slit so that the laser attenuator could slide in and out more easily.

Modification of the laser attenuator slit with a razor blade

• One small note on the laser attenuator: it is difficult to determine which opacity you have it set to, since you cannot easily see into the aperture when the cuvette holder is assembled. This could be a problem if you are trying to compare methods with other scientists, or even just to achieve consistency within a single testing session.

Laser attenuator

My fully assembled kit

Calibration:

• I found that pointing the spectrometer directly at a CFL bulb, even from a distance of several feet away, always resulted in overexposure of my spectra.
• I had success using light reflected from a piece of plain printer paper, as suggested in the calibration notes.
• I noticed that, for some reason, reflected light did not activate the “CFL detection” icon in the spectral workbench interface, even though the peaks appear to be much the same.
• In my first attempts to calibrate the spectrometer, the instability of the camera was a major stumbling block. After noticing that the calibration was shifting (sometimes dramatically) between consecutive spectra of the same CFL bulb, I opened up the spectrometer's housing and found that the camera was no longer firmly mounted to its foot. After re-mounting the camera, I was able to get much better replicability over several spectra!

Replication of CFL spectra when camera is securely fastened

Comparison of overexposed CFL spectra with proper exposure from reflected light

• I think the calibration procedure on Spectral Workbench should be modified to specify which green peak to use for calibration, since there are two peaks roughly corresponding to the “mercury 3 line,” falling 4-5 nm apart from each other, as discussed in a prior research note.

Thanks! I look forward to working with all of you on this exciting project.

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Week 3: Recap from Oil Testing Kit Beta Program weekly chat

by warren | over 8 years ago | 3 | 0

Hi, all -- we had a quick chat today and folks are preparing samples and troubleshooting the scanning process. Please post your data as you go, and/or ask for help on the spectrometry list (see in sidebar to left)!

Dilution

We noticed that the procedure described in the wiki did not go into detail about how and when to dilute samples, which can help if they are too dark for the fluorescing light to make it through:

http://publiclab.org/wiki/oil-testing-kit-beta#Procedure

The gist is, you may need to dilute crude oil or its density will actually dim the fluorescence it produces. Be aware! You can read about my own dilution documentation in the test I did some time ago.

I also added an explicit step to scan pure mineral oil, so that you can confirm that it does not fluoresce.

Baby oil

Last week, we talked about alternatives to mineral oil as a solvent. At LEAFFEST 2015, we explored some possible problems with baby oil, if it has added vitamin E -- and linked back to some old research about how vitamin E can occur in fish oil, complicating scans for polyaromatic hydrocarbons there. Neat stuff; read about it here.

Finally, it sounds like some folks are having some lingering assembly and calibration issues -- please don't struggle in obscurity! Post and ask questions here in the comments, or on the spectrometry list!

Thanks, and hope to see some uploaded sample scans soon! Remember to tag them oil-testing-kit and good luck!

The transcript of the chat follows:

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Vitamin E fluorescence in some baby oils -- and relevance to the Oil Testing Kit

by warren | over 8 years ago | 0 | 1

False positives

Since we use mineral oil in the Oil Testing Kit as a non-fluorescing solvent, I was surprised and concerned to see that some baby oils contain vitamin E additives, as the label of the above-pictured bottle indicates! Some folks have mentioned using baby oil as a widely available source of mineral oil, and although it sometimes has fragrances added, the baby oils I've used do not fluoresce on their own when a 405nm laser is shone through them.

But as we learned from a great poster by co-author Edwin Pena of Seton Hall University:

...vitamins E and A can give you false-positives for PAH contamination when using UV fluorescence to assess presence of PAHs...

My attempt and results

So, as @cfastie had a bottle of Vitamin E enriched baby oil at LEAFFEST 2015, I tried it out -- pictured above. I did not take a spectrum of it, but perhaps Chris will. In any case, there's clear and relatively bright visible fluorescence (I was wearing yellow glasses and did not look at it directly, no worries!).

Questions and next steps

OTK users should know that they have to check baby oil for fluorescence before using it as a solvent to dilute samples.

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