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ASSISTANT LAB OFFICERS REPORT

Heather Barnes

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SUMMARY

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Individual Measurement Systems

velocity gantry

The Velocity Gantry was not used to measure samples from this expedition, but was tested several times for the KTLF. No problems were encountered during the testing process: correct data were acquired and uploaded to LIMS.
The only minor issue is at the beginning of the expedition when the PWAVE caliper was found to be stuck in the closed or home position. As the limit switch was triggered, the manual control buttons to the left were inoperable. To solve this issue, the limit had to be unscrewed loose and the Exlar software used to open the actuator.

Moisture and Density (MAD)

No samples from this expedition were analyzed at the MAD station. However, it was significantly tested for the KTLF exercise, in light of the new web services deployed. Routine calibration of the pycnometer was included in the testing routine.
Several bugs were reported, but were all addressed as of the writing of this report, with the latest MADMax version being 2.2.0.19

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The cells will now run at ambient room temperature. Pre- and post-modification calibration and verification measurements of the cell and standard sphere volume indicate differences that are less than 1% compared to legacy data (cf. file:///:\{color:#548dd4}IODP_Share_362T_test_folder\Physical Properties\MAD (see subfolders)\MAD Pycnometer\Pycnom CalibVerif_EXP362T.xlsx). Cell volume is higher across the board by 0.6%, but the ratio of cell to expansion cell volumes are on the average only 0.03% higher for the current set-up. Normalized volume of standard spheres also indicate a higher estimate but by only about 0.1%.
However, despite this initial demonstration of comparable and still accurate volume estimates with this new pycnometer set up, it is highly recommended that the upcoming expeditions regularly perform, closely monitor, and document the calibration and verification measurements, taking note of any temperature-related effects on the values.


Close-up photo of the Tygon circulation tubing of pycnometer #4, clogged with organic growth that is preventing water from circulation through the cell.

FLIR image of the pycnometer cells with warm (55°C) water pumped through the series, showing that the water is only able to circulate through cell #3 because all other cells have clogged tubing.

1. The combined volume of the 200 and 300-series of standard precision balls used in calibrating the pycnometers is changed from the 10.2 cc to the more accurate value of 10.255 cc indicated in the actual calibration certificates (cf. IODP_Share\PhysProps\ Certificates\MADMAX\Precision Ball calib certs.pdf and IODP_Share\PhysProps\MADMax stuff\Precision ball calib cert.xlsx).

Table 1: Comparison of parameters estimated using pycnometers with or without circulating water temperature control.

Shear Strength Station (avs)

IT'S ALIIIIIVE!!!
Thanks to Erik Moortgat, the AVS is now working again! Below is the narrative of the troubleshooting process that he underwent.
"It was reported to me that the AVS Giesa system had not been working for a couple of Expeditions and since I had worked on it before I was asked to take a look. Sure enough, the Giesa application would not start at all.
I sent some information to Giesa mbH, primarily about concerns about the environment (Windows/Office), but they said it should work fine as such. So I decided to do a complete clean install of the software. The Giesa application could now run!
The next issue was the inability of the FL2 to talk to the Excel spreadsheet required to record the data. None of the templates we had on the PC would work. The FL2 was working, blade was turning and there were bits of data going into the sheet, but we were not getting the updates at the frequency specified. Another e-mail was sent to Giesa mbH and what we learned is that the tab order in the template was critical. Since our FL2 is running on COM2 of the PC, the main tab, Flügelversuch, has to be in the second tab position. So the template's tab order has to look like this:
Tabelle1, Flügelversuch, Tabelle2, Tabelle3, …
When you save the sheet as a csv, for upload via MUT, the main tab, Flügelversuch, has to go back in the first order position. Also, the file name has to end as …avs.csv (e.g. TextID_avs.csv). I think that everything else from the QSG stayed the same."
Additional notes about uploading data: To identify the sample in the Excel file, enter the TextID right of the cell labeled barcode. Otherwise, use the scanner, but make sure to cut out everything right of the Text ID and paste it to the adjacent cell to the right (2^nd cell to the right of the barcode). Remember to enter the offset in the appropriate cell below, not necessarily in the filename after the textID.
The Penetrometers and Torvanes were also found to be in good condition during the KTLF assessment.

Special Track Multisensor Logger (STMSL)

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from the STMSL was collected during this expedition. However, test runs for the KTLF showed no problems with the instruments, data capture, upload and reporting process. As of the writing of this report, the STMSL is running with IMS v. 9.0

Whole Round Multisensor Logger (WRMSL)

The WRMSL was upgraded to IMS v 9.1 during 362P2. Two code-related issues were encountered and resolved. Other than these, the WRMSL is running well, even with the new web services.

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Solution: Bill Mills sent instructions on how to fix this behavior. The VI that caused the transformation from underscores to dashes was removed. It is nested very deeply in the section of the code that writes the data files. Since it was actively converting underscores to dashes in the (wrong) spot during data file creation you would never have found it by searching for "PWAVE-L" strings in the static code itself. That's why the config file edit attempts weren't working either.

Section half image logger (shil)

The SHIL was used for both archive section half and whole round line scan imaging.

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1. Unfortunately, the RGB offset issue from Exp 355 has made a reappearance. This issue is best described as the RGB data being recorded starting at offsets about 3.5 cm from the top of the section, and running past the end by about the same amount. This was fixed by Bill Mills during the pre-Exp 356 tie up but we could not lay our hands on the solution to date. Awaiting Bill's return for this problem.

Section Half Multisensor Logger (SHMSL)

The SHMSL was used to scan all section halves collected during 362T.

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1. During the KTLF testing, it was noticed that the zeroing point of the MS2K is about -10 units off compared to a blank measurement at the level of the section half surface. This was attributed to the significant distance between the zero point and the section half surface relative to the 2x2 extruded aluminum bar frame below. As such, David Houpt changed the zero point from 3 to 1 (in Motion>Setup >Fixed Positions> Load and Unload). This allows the MS2K probe to zero at a level similar to the section half surface and at similar relative distance to the extruded aluminum frame. Though the frame still has an influence on the measurement, at least it is low enough and constant throughout the track.
2. It also appears that the zeroing step occurs about the same time as the gantry moves to the first measurement point, akin to an old behavior that was rectified, but is now back. In order to minimize or eliminate all possible sources of error, a time short delay should be placed after the zeroing step, prior to moving to the first measurement point.
3. Aluminum, although paramagnetic, is displayed by the Bartington meter as if it is quite diamagnetic (gives high negative susceptibilities when aluminum is placed close to the probe). As such, the aluminum mount for the laser and the hefty aluminum ruler were replaced with Plexiglas versions. Many thanks to Etienne for his craftsmanship on both pieces.

Natural Gamma Radiation (NGR)

The NGR and NGR Master operated without problems under the new set of web services. Instead of the normal 300 s per position, data for Exp. 362T were collected at 900 s for each of the 15 sections in order to be consistent and comparable with those acquired during Exp. 360.

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1. Discussions about the NGR legacy data mining exercise continued, particularly on the use of only the 1^st position of the background measurement when doing data reduction. One quick validation experiment was made on 31-7-2016 to collect background data with the data reduction engaged. Result indicates counts of less than 1 per second for detectors 2 to 7, whereas the outermost detectors 1 and 8 were about 1.2 counts per second. This close to null background value demonstrates the importance of NOT REDUCING the data when doing background measurements. More discussion will have to be made on a more efficient and way of collecting and applying the background data.

Thermal conductivity

No thermal conductivity measurements were made on the newly acquired cores. However, KTLF testing showed that the system is functioning. Moreover, a long-time file re-naming "bug" has finally been understood and corrected!

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1. The objective used is different from what is selected in the ImageCapture program.
2. The newest microscopes in the JR, the Axio Scope.A1 and the Axiophot, are equipped with a tube lens turret (Optovar) with magnification lenses of 1x, 1.25x, 1.6x and 2x. A setting other than 1x would previously have resulted in a scale bar shorter than what it should be.
3. The ImageCapture program invokes a vendor-supplied module (SPOT software) to set and control the CCD/CMOS camera and capture an image. One of the many functionalities of this module is the ability to define a region of interest, thereby using only part of the sensor/chip area (Fig. 1). If this is selected, the result is a variably underestimated scale bar (Fig. 2) that is a function of the area selected.

Figure 1: Screenshot of the SPOT module configured to image a subset of the full chip view

Figure 2: Screenshot of the ImageCapture window showing the erroneous scale bar for an image captured using only part of the CCD chip. Longest tick mark interval is 1 mm, making the image almost three times bigger than for a full-chip image.

Also, previous calibration methods involved imaging a micrometer using the various objectives attached to a particular microscope. The image width or "field of view" is then measured. The values are then extrapolated to a magnification of 1x to derive a factor used in calculating the number of pixels per mm. However, the micrometer has an accuracy of only 0.02 mm and the imaged tick marks may vary in thickness depending on user settings in acquiring the image.

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The total magnification value of a microscope-camera set-up is a product of the objective magnification and other intermediate lens accessories in the ray path to the camera. The new Axio Scope.A1 has a lens turret (Optovar) with magnification lenses of 1x, 1.25x and 1.6x (Fig. 3 top photo). The SteREO Discovery.V8 stereoscopes have a more variable magnification anywhere between 1x and 8x, and a camera connector tube with a magnification of 0.5x. At present, Image Capture v. 4.0.0.1 is not set up to capture these intermediate magnification values. As such, "virtual objectives" are now inserted in the configuration file (see Appendix A and B):
Figure 3: Photograph of the intermediate lens turret module (Optovar) for the Axio Scope.A1 (top) and (bottom) the zoom knob of the SteREO Discovery.V8 with preset zoom values and the screw on the side of the knob for adjusting between continuous and discrete zooming

For the Axio Scope.A1, these "virtual objectives" should be modified when a new objective of different magnification is added to the nosepiece. For the SteREO Discovery.V8 stereoscopes, the "virtual objective" magnifications are calculated for only the discrete zoom values set in the control knob (Fig. 3 bottom photo). Anything between these pre-set values would create an inaccurate scale bar. To aid the user, the zoom knob should be set to click on these pre-set values by turning the side screw to the recessed position. Nonetheless, the ability of continuous zoom for any stereoscope is always an ever-present source of error in calculating the scale bar.

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