Introduction and method overview

This user guide contains standard operational procedures for the Scanning Electron Microscope Image Uploader (SEM Uploader). The workflow for working with the SEM is as follows: 1) take pictures on the Scanning Electron Microscope, 2) save the pictures and the associated metadata on the PC that runs the SEM software 3) transfer pictures and metadata to the IODP LIMS database using SEM Uploader and MUT.

Upload

After taking the images on the SEM and saving them on the PC (please follow the image naming convention below) 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 MegaUploaldaTron5001 (MUT), 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 (Figure 1).

Figure 1. SEM Uploader user interface.

4. Select image and click Process, OR click Exit if you decide to upload later, OR click CLEAR, which will clear out the image from the selection. Select another image right away if the one chosen is not the one that you wanted to upload.

Potential errors:

Image type is one that is not produced by the SEM (Figure 2)

Figure 2. SEM Uploader message if a NON-image file (JPG, PNG, or TIF) is selected.

Image has no metadata .txt file (Figure 3):

Figure 3. SEM Uploader message if a selected image file has no metadata file

Associating images with samples:

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 4).

Figure 4. The second SEM Uploader window.

In Hierarchy search, click through Expedition/Site/Hole/Core/Section/Section Half down to the sample that the SEM picture was taken from. The sample will be validated automatically with Text Id and Sample Id. 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 5).

Figure 5. Text ID search validation of an invalid Text ID will notify the user of the mistake.

Adding sample categories and comments

The user now needs to pick a Category from the drop-down list. The red asterisk next to the category field indicates that this field is mandatory information. The rest of the information is not. The user can pick a general subcategory and if the expedition has an expedition specific subcategory associated with it this field will auto populate. If there is no expedition specific subcategory, the field will be greyed out. The user will then be able to select a value from the drop-down list. However, if the desired value is not in the list, it cannot be added by the user. The user will need to ask the description technician to add it to the drop-down list. The user has the option to add comments as well. The comment field allows up to 200 characters without restrictions on special characters. There is also an option to enter initials in the Image creator field.

Uploading to the database

The Upload button is activated once the user has filled out the sample selection and picked a category. Clear will clear the sample selection as well as the selection of descriptive parameters. Cancel will navigate the user back to the first file selection window where the image was chosen. MUT should display the ".SEM" uploader file in the user interface after the user clicks upload. If the directories are set correctly and MUT is working properly the files should be uploaded to LIMS right away. Contact a technician if you see any issues.

Download from the database

The SEM report can be found as part of the image reports in the LORE interface: http://web.ship.iodp.tamu.edu/LORE/

To select an SEM image the user must click on 'Images' under 'Select report' and then select the Scanning Electron Microscope (SEM) option. Users can decide to use the standard (commonly used for viewing and downloading data report) or an expanded report (used for data review to see all information captured). 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). Once the hierarchy is picked, click "View data" – all the available SEM images for that sample will be listed. Each sample has a unique Text Id that can be found on the sample label in both barcode and human-readable format. 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.

Naming and Saving Conventions

Naming convention for SEM files:

EXP number
Site
Hole
Core
Section
Sample
Taxa/specimen/piece
No. 1, 2, 3, ….

E.g.
349_U1431A_1H_1_10-11cm_Emiliania_huxleyi_1,
349_U1431A_1H_1_10-11cm_Emiliania_huxleyi_2,
349_U1431A_1H_1_10-11cm_Emiliania_huxleyi_3, …

Storage convention for SEM files on the local PC:

SEM
1. Site
2. Hole
3. Sample

E.g.
Folder SEM
Folder 1431
Folder 1341A
Folder U1341A_1_H_1_1-11cm (all files for this SEM sample)

All those files need to be moved to USERVOL and DATA1 before the end of the expedition.

Credits

This document originated from Word document SEMUP_QSG_374_DRAFT.docx (see Archived Versions below for a pdf copy). Credits for subsequent changes to this document are given in the page history.

SEM File Uploader Quick Start Guide (no longer used)