EXP 391 Imaging Tech Report

Owned by Former user (Deleted)
Last updated: Feb 02, 2022 by jr_crowder
7 min read

Sandra Herrmann

Summary

Expedition 391 started as a full-length expedition with a full technical and slightly reduced science staff. The material recovered ranged from ooze to sandstone to volcanoclastics to basalt. All WRND sections that were hard-rock curated were imaged and proofed (1100 WRLS) and 285 WLSC images were created and uploaded by the Imaging Specialist. 889 SHLF images were proofed, 114 CLOSEUPs as well as 160 PICAT images were created. COREPHOTOS were automatically created by the PUBS Specialist. The scientists were introduced to ImageCapture for MICROIMG and SEM image usage/upload.

I trained a new member of the technical staff as core description technician and provided support throughout the expedition  ranging from in-depth training in DESClogik, Thin Section Writer/Builder, data management and sciecne support.

The Imaging lab produced nine weekly family and friends photo series with 245 images total, orchestrated the logo printing party and took care of all microscopes setup/maintenance, the SEM as shared responsibility with the core description tech.

List of general imaging duties/services provided

  • Headshot posters

  • Download and proof line scan core images

  • Shot close-ups

  • Production, editing, capturing and shipboard approval of the weekly photos

  • Production of group photos

  • Printing of T-shirt logo

  • T-shirt printing party

  • Clean and adjust microscopes, change and center objectives etc.

  • SEM introduction, upload of images and assisting in usage

System Status

PICAT -

A light bulb was replaced. No other issues have been encountered during this expedition.

Closeup Station -

Closeup worked well - data transfer interruptions have been encoutered. Hence a data cable has been replaced and two new one's of the same kind ordered.

A chart for decision making in close-ups was developed and added to the lab. It is available on the Imaging lab confluence page.

Fig. 1: Close-up decision help.

The data connection on the camera, that was used on the CLOSEUP station (Cananon EOS D5) is lose in the socket. The ET tried to repair it. He was not successful. The camera is being send back to shore for evaluation.

Fig. 2: Lose socket on data cable connection.

SEM -

The SEM was used by paleontologists and sedimentologists during this expedition. Images were uploaded by technician and science party.

Microscopes -

Microscopy methods were added to confluence to give a better idea of transmitted and reflected light as well as Polarized, Darkfield, Phase, DIC. New objectives were added to the inventory on confluence and labeled.

Setup of microscopes

Stations were set up by for basic observations at the beginning of the expedition. During the first days of actual operations, the scientists reevaluated and changed specification, so they had to be adjusted. Rotating stages were requested for all scopes. Unfortunately, we couldn't run the lab to full capacity since one rotating stage is still in transit back to the ship after repair.

The objectives were centered every few weeks during the duration of the expedition (all of them).

One new Axio Imager 2 scope was set up by the off going crew, one more was put together and staged in the FIMG office.

Maintenance

Two of the older light source had to be repaired by the ET as the wires from the bulb holder to the cable were brittle/burned. The Imaging Specialist pulled all light sources of the same kind and asked to check the weak spot on each one. The ET replaced and secured each connection. Additionally, the feet of two of the light boxes were half melted (maybe from Acetone, not sure) or had moved over the venting slits over time. New feet were printed and attached by the ET.

Fig. 3: Corroded wire on light source and new feet on light boxes.

Special microscope project

I was tasked with figuring out if the Zeiss cameras can work with ImageCapture and/or to find alternative methods to work it into the workflow for microscope users. An email chain explaining that the Zeiss cameras can't work with ImageCapture - received from James Zhao, the developer I worked with, can be found here. Hence, the ImageCapture integration is not a possibility.

Further research shows that the software used on the Zeiss cameras, is able to export the following file formats:

.czi - a Zeiss-specific format, that can be read by ImageJ, Python and Matlab, as well as several biotech programs,

.jpg, .jpeg, .png, .tif and .tiff - regular extensions

Metadata files are exported as .xml file.

An extra folder was created in the Imaging Lab confluence page to store examples and additional information. It seems promising that the image upload to LIMS could be accomplished with interfacing python and Angular to create an interface that looks similar to other image uploaders used in the labs. Further research is needed to explore the detailed requirements.

SHIL -

Overall, the new lights are an immense improvement over the previous setup. I applaud the team that worked on this!

After giving a general Imaging Introduction talk during the hotel quarantine and a few meetings discussing the implications of wet and dry imaging on the workflow n the lab, A graphic SHIL help guide was developed and added to the lab. It shows what the science party decided for wet/dry scanning of samples and adds general tips. It is available on the Imaging lab confluence page.

Fig. 4: SHIL help guide.

Issue 1: Instrument_group assignment was switched to IMG

The first scans from the SHIL didn't show up in LORE/LIVE as the instrument_group was set to IMG, instead of SHIL. The error was resolved and the developer reassigned the LSIMG to the correct samples.

Issue 2: 360 scanning setup - not enough space, same for switching between holders

The distance between the new camera-light housing (the protective black shielding) leaves a very small space to exchange SHLF and WRND sample holder (see pictures). It is doable, but the constant switching causes either that the housing or the holder/QP standard gets scratched/bumped. Is there a way we can solve this? Currently, the holders get loaded from the front. Can they be slid in from the end? Can the part, that the holders slide in, be on hinges so it can be temporarily lowered to install/switch sample holders?

Fig. 5: Limited space for WRND sample holder and scratch marks on the QP standard resulting from the limited space for sample holder switch out.

Issue 3: Whole-round sample information still not showing

The WRND sample information is not displaying when scanning the QR code on the label, sometimes it shows the samples when the LIMS tab hierarchy selection is used.

Special SHIL Project

WRND sample scans were performed for a shore request - both on 45 and 60 degree rotations. The goal was to evaluate the difference in edge distortion of the images when scanned in smaller segments compared to the 90 degree segments currently used. The image quality improvement is marginal.

Fig. 6: 45 and 60 degree interval scan experiment.

Photography

Cameras, camera lenses, flashes were inventoried on confluence. Imaging lab drawers were organized to group equipment by use and manufacturer.

Printer Epson Stylus 4900 -

not on board. It is supposed to arrive on the ship for the upcoming expedition.

Printer Epson ecotank -

The ecotank was working like a champ. It was used to print all group photos and T-shirt logos.

Software Suggestion

SHIL -

Just like last time, START screen in LIMS configuration could be sorted with latest site/hole on top of the list. 99% of the time that is what the person using the system wants to scan.

Items Received

  • Ink bottles for Epson ecotank printer

Items Shipped to shore

  • Canon EOS 5D Mark II with broken board

Items Ordered

  • Data cables for PICAT and CLOSEUP station

  • Four books for Imaging Lab

  • Camera sensor cleaning swabs

PR images

A total of nine weekly photo series were created, edited, tagged, captioned, approved by shipboard leadership and transferred to shore.

File Storage

LSIMG (889), WRLS/WRLSC files (1100/285), PICAT (180), CLOSEUP (114) were stored on LIMS. RGB and ROI files for all holes were saved on data1, folder 26.1 RGB.

PR images were carried home on external hard drive and stored on the NASIMG.

Miscellaneous projects/tasks

A new SOP was reviewed and is still being developed by TAS supervisors, LO and the Imaging Specialist.

A mini project for an improved 360 uploader was submitted to TAS management.

I tested the upload of images to MerlinOne and uploaded the 396T group photo as well as other weekly photos. I worked with M. Berardi on setting up the correct privileges for the Imaging Specialist for MerlinOne.

Support for upcoming expedition was provided as much as possible (mugshot templates, ID cards, microscope setup etc.).

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