EXPEDITION NOTES

Expedition 392: Agulhas Plateau

Microscopes

Activities

1. Set up binocular microscopes for polarization, phase contrast, differential interference contrast for use by nannofossil, diatom and pollen micropaleontologists and petrologists. Given the variety of requested settings and fixed number of accessories, the Axio Imager A2 set up in the Imaging Lab was exchanged with one of the SteREO Discovery in the microscope Lab. The lone foraminifera specialist requested for a 1.5x stereoscope objective and the Image Capture settings was updated to reflect the product of the various zoom settings.

Issues

1. Polarizer holder on one of the Axio Scope A1 was found to have a broken locking pin. Removed as user does not need a polarizer. No spare onboard. Need to purchase Polarizer D, 90 rottable, removable (Zeiss part 427706-0000-000), or, check if there are spares on shore, even for the old accessories (we used to have a lot).

2. A nannofossil scientists wanted to use a circular polarizer, which we do not have in the inventory. Request to purchase for future expeditions a circular polarizer D, fixed with lambda/4 plate, rotatable (Zeiss part 453623-0000-000).

3. All 5 quartz sliders (0-3 lambda) are delaminated. The least damaged slider was used by a nannofossil scientist during the expedition. Request to buy spare Quarz sliders (no part number in latest Zeiss manual).

4. Image Capture continues to be interrupted by unexpected error/unhandled exception related to Atlasoft which would render the application to not start or acquire image. The developers are aware of this ongoing issue and have advised users to close and re-start Image Capture when the problem arises.

5. Newest Zeiss Axio Imager.A2 (SN: 3527004117) cannot be powered up, only momentarily after the switch is flicked. Initially contacted Brian Walsh (Account Manager) and Customer Support/Sharon. Apparently, a Zeiss engineer suspects "that it may be the battery on the main board or the main board itself is bad". However, the initial diagnosis was for the motorized stand and not for the manual stand that we have. Eventually, Nelson Mendoza of the Zeiss Technical Support Group guided us in troubleshooting the microscope, and lead to the conclusion that the internal power supply (Part No. 000000-0457-273; ~$684) needs to be replaced. The part was ordered and received by G. Giesecke on March 7, 2022 and will be sent to the ship via airfreight.

6. The coarse adjustment knob seized on the Axiophot ("Kiwi"): the fine adjustment knob rotates, but the stage remained in place. The knobs and Geneva gears were removed and found to be fine. This required a deep-dive into the assembly, removing all accessories and opening the bottom panel to access the gear mechanism. It was found out that the inner, larger-diameter segment of the main focusing shaft was forced into the smaller diameter hole of the black, stationary circular retaining ring bolted into the main frame. With the stage removed to free-up some weight, the main shaft was gripped with a pair of pliers and carefully and slowly rotated out of the bind. With the main shaft freed, the coarse and fine adjustment focusing knobs now synchronously work. Given the permanent groove on the focusing shaft of this Axiophot, it will be more prone to future seizing and therefore require more gentle handling, especially that it is the best microscope in the inventory.  Please remind future users not to force the knobs beyond their limit, given that some might be familiar with a counter-rotation technique of fixing adjustment knobs, but is only applicable to certain brands and models.

Open

Received

1. Maerzhauser XY stage EK75x50, repaired by Serco Technical Services (1 pc)

2. Zeiss illuminator microLED 2 for mounting on lamp interfae for transmitted or reflected-light illumination (6+1 pcs)

Exp 391

• new objectives inventoried and new microscope stashed away in the Imaging office

• Status: Zeiss camera software is able to produce jpeg, jpg, png, tif, tiff files and xml metadata files, developer working on integration into ImageCapture

• Info: new scope in FMBIO is using the Zeiss camera because we have no workflow to put microbio images into the LIMS; those (if any) are saved to DATA1 without any database involvement. The new scope for CMIC should have a SPOT camera attached to it so it can be part of the normal LIMS image capture workflow.

Exp 390R

SHIL Testing

A copy of the SHIL Report prepared by Sarah can be found by clicking the link here: SHIL Report 390R

• A spacer was put between the two brass blocks on the SHIL to put the lights at a 45° angle in hopes to reduce reflection in cores. Initial testing by Imaging Specialist showed some reflection reduction. A side effect of angling the lights is less light passing through to the camera. To compensate the f/stop was changed from f/22 to f/16.

• The spacer allows for an even slit passing light through to camera. Previously, owing to face-plate screw locations, the brass blocks diverged slightly and was seen as a possible cause for image grabs with consistently darker right sides. ←double check to see if fixed.

Jai Camera Meeting

12/18/20: Had a meeting with JAI to discuss camera setup and calibration procedures. Notable things that came from the meeting:

• During calibration, exposure and gains should be set prior to doing camera corrections.

• The order of camera corrections should be pixel back, shading, and pixel gain. Our procedures had put the pixel black correction last. This has been amended in the manual

• Shading Correction: best to use a white or light gray sheet and slowly move the camera back and forth. This helps average the pixels and should help with the streaking in our images.

• He indicated the more we increase our gain the more noise we will get in our images, another amplifier of image streaking

• The 'green flash' we saw in the J1007C  Camera was a known issue for them and supposedly resolved with firmware upgrades by auto-resetting the trigger if it hasn't gone off in a while.

• The green line (green chromatic aberration) seen in the QP Card at the top of the scan could be a result of both the prism inside the camera and the lens we use (35mm). It was recommended to try a 50mm lens. To date, we have not tried this. It was also mentioned that one of their newer cameras auto corrects for these aberrations. He pointed out that just because we only see it in areas of high contrast, it's likely that it's present throughout the scan.

• We asked questions about our lighting system and he recommended we communicate with ProPhotonix. They have off the shelf and custom LED line light solutions for line scan imaging, including RGB sensitive line scanning.

• Imaging Specialist will continue communicating with JAI and ProPhotonix after the holidays.

[ X390C ]

X390C

Exp. 382 Iceberg Alley

• Shutter assembly on one of the Cannon 1D cameras had come loose and the LCD screen showed Err 20.  Etienne was able to get the shutter back in place and clear the error.  The camera has had no issues since.

Microscopes

• Micrometer slide KR-812(1x3) was broken under an objective during routine field of view calibration.

• Axio Scope.A1 (#90818) XY stage screw came loose. In one instance, it also had a partially blocked field of view even if all accessory lenses and filters appear to be in place, but was cleared when the binocular tubes were adjusted. This might indicate a loose intermediate lens along the illumination path, which can be looked at in more detail during the next service call.

• The microscope cameras often become unresponsive, giving a "Busy camera" pop-up message when a user attempts to capture an image. This happens if the camera was previously being turned off BEFORE closing the ImageCapture or SPOT software,

• A micropaleontologist inquired about setting up one of the newer model Axioskops for differential interference contrast (DIC) method, often used to observe diatoms. At present, we only have the Nomarski lenses for the objectives of the Axioplan2 Imaging microscope, currently set up for fluorescence microscopy (MBIO). The accompanying 63x objective is no longer in the inventory, so a new one has been ordered. For future expeditions that require the DIC method, the Axioplan2Imaging can be moved to or swapped with a unit from the Microscope Laboratory.  Note that the new models of Zeiss microscopes may only support PlasDIC, the new version of the classical Smith/Nomarski DIC (cf: http://microscopy.berkeley.edu/courses/TLM/dic/dic_vs_plasdic.html). For related parts and variants of the Axio Scope.A1, see https://www.micro-shop.zeiss.com/en/us/system/legacyredirectsystem/10183.

Exp. 378T

• Replaced coolLED 585 and 490 nm and combiner for the MBIO microscope. During the previous expedition (385) very distinct "web" artifacts appear in the field of view and images taken, despite refocusing the light sources. The new 490 nm light source still show this artifact, but fainter. We are awaiting follow-up replied from coolLED (as of Dec. 2, 2019).

• The 10x10 gridded reticle (KR-406; 26mm) is missing. This reticle facilitates counting of microbiological specimens. Two pieces are currently being ordered. 

Exp. 378

• Image capture scale calibration on scope A.1 in the smear slide area of the lab was found to be incorrect when compared with the micrometer.  The scope was installed in Punta Arenas, and the issue was likely occurring throughout Exp 385.  The scale label placed next to the scope was also incorrect.  The scale applied to the image with image capture is about .82cm instead of 1 cm.  Programmers working to recalculate scale.  This issue was noted on a second scope as well, but to a lesser extent.