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User Guide
Manual Information
Author(s): | S. Herrmann | |
Reviewer(s): | L. LeVay | |
Manager Approval (Name, Title, Date): | D.J. Houpt | |
Audience: | Scientists, Laboratory Technicians | |
Origination date: | 06/07/15 | |
Current version: | V374 | March 2018 |
Previous versions: | V1.1 | June 2015 |
Domain: | Description | |
System: | Scanning Electron Microscopy | |
Keywords: | SEM, TM3000, image, |
User Guide Contents
Topic | See page… |
Introduction | |
Method Overview | 2 |
Software Required | 2 |
Admin and developer support | 3 |
Upload | 3 |
Download | 6 |
Tips | 7 |
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Introduction
This user guide contains standard operational procedures for the Scanning Electron Microscope Image Uploader (SEM Uploader).
The description technician performs maintenance and an introduction of the SEM for scientists. Information on the SEM itself is presented in the SEM User Guide (digital on the SEM PC and as print out next to the SEM) provided by Hitachi.
The SEM Uploader software is an in-house development that makes it possible to upload the images and metadata from the SEM to the IODP database LIMS. SEM Uploader works in combination with the MegaUploadaTron5001 (MUT).
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- Take pictures on the Scanning Electron Microscope
- Save the pictures and the associated metadata on the PC that runs the SEM software
- Transfer pictures and metadata to the IODP LIMS database
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Software required
SEM Up
SEM Up is the software that will prepare the original SEM pictures and metadata file for the MUT uploader. It will create a MUT uploader file (see Figure 2 column "Filename" on the MUT user interface) that is formatted in a way MUT can read. SEM Up will extract some of the metadata to this MUT uploader file in order to display this metadata in the LIMS search.
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The MegaUploadaTron5001 (MUT, Figure 1) is the software that will upload the SEM pictures and metadata file to the LIMS database. The program needs to be installed on the PC and up and running in order to have a successful upload take place.
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Figure 2. MegaUploadaTron5001 (MUT) User interface.
Admin and developer support
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The General subcategories in SEM Up represent main value lists in DESClogik. If any of the components has a sub value list that is specific to the expedition created, this must be communicated to the developers. The developers will then associate this expedition-specific value list/subcategory with the appropriate subcategory in the SEM Uploader.
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Upload
After capturing the images on the SEM and saving them on the PC (following image naming convention) the user is ready to upload the pictures to LIMS. These are the steps for preparing the files for upload and initializing the upload:
- Open MegaUpoaldaTron5001 (MUT) and login to the current expedition or project. If more information is needed, refer to the MUT manual.
- Check if the correct uploader directory is set (go to File, Set Upload Directories). By default, files to be uploaded by MUT are saved to C:\DATA\in.
- Open the SEM Uploader.
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The second window is designed to associate the sample with the image. There are two ways of assigning the sample – hierarchy search or Text ID search (Figure 6).
Figure 6. The SEM Uploader window is the place to assign the sample to the picture as well as additional information about the specimen seen in the image.
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In the Text Id search, the user enters the known Text Id into the blank field and clicks Validate Text Id. If the user picks an invalid Text ID, the SEM Uploader will tell the user (Figure 7).
Figure 7. Text Id search validation of an invalid Text Id will notify the user of the mistake.
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Here are examples for adding descriptive metadata to the SEM image:
CATEGORY | FOSSIL | LITHOLOGY |
COMPOSITION | ||
GENERAL SUBCATEGORY | calcareous nannofossil | sediment |
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EXP. SPECIFIC SUBCATEGORY | calc_nanno_333 | sediment_345 |
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VALUE | Emiliania huxleyi (Lohmann, 1902) | clay [Leg210] |
olivine |
As you can see, some categories have no additional general subcategory. The field will be greyed out in this case. In the case presented, category composition has neither a general subcategory nor an expedition specific subcategory. The value drop-down list will simply have all entries from the category list composition listed.
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To use the hierarchy search, click the "Select by Hierarchy" tab on any sample module. The hierarchy search allows the user to progress through the sample hierarchy tree (expedition, site, hole, core, section, section half, etc.) to focus the search to the desired level.
A hierarchy search can be combined with a parameter search (such as sample type) to narrow results by browsing down the hierarchy (at least to the Hole level) and then adding specific search parameters. This can be done in any order. Combining searches may result in a too-narrow query that may return no samples.
Each sample has a unique Text Id that can be found on the sample label in both barcode and human-readable format. The Text Id for each sample can also be found in LIME. Specific samples (and their children) can be found using a TEXT_ID search. Text Id's can also be found in the Sample search in LORE/LIMS and SampleMaster.
To search for samples by Text Id, click the "Text ID Search" tab on any sample module. Enter one Text Id manually or paste from a list into the entry field. Once the Text Id is entered, click "View data" – all the available SEM images for that sample will be listed.
A Text Id search can be combined with a parameter search (such as sample type) to narrow and then adding specific search parameters. This can be done in any order. Combining searches may result in a too-narrow query that may return no samples.
Tips
- Upload is independent of the capture process so multiple images can be taken and only the ones desired can be uploaded,
- Comments can be seen in reports so make them useful for your later need.
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