Table of Contents
Phase-contrast image of a discoaster taken onboard the JOIDES Resolution during IODP Expedition 355 (Arabian Sea Monsoon). Image taken by D. Kulhanek.
Introduction
This document provides an introduction to using the SPOT cameras and Image Capture software used on the JOIDES Resolution.
Procedures
- Turn on camera (Figures 1A and 1B). Make sure the slider on the microscope is pulled out (Figure 1C) or the switch is set to the camera position (Figure 1D) to allow light to reach the camera. Trouble connecting? If the camera was unplugged while the software was started, you might need to restart the computer. Sometimes, Windows doesn't recognize hardware unless it is plugged in and restarted.
Figure 1. Shipboard microscope cameras. A. SPOT idea camera on stereoscopes. B. SPOT camera on transmitted light microscopes. C. Slider to switch light from oculars to camera on transmitted light microscope. D. Lever to switch light from oculars to camera on stereoscopes. - Open Image Capture software on computer and login with username, password, and expedition number.
Figure 2. Image Capture software interface. - Select the sample by clicking on Browse (red box, Figure 2). You can search by Sample Types, analysis type (Test List Selectors), or both (green boxes, Figure 2).
Select the sample from the sample list (blue box, Figure 2) and close the browser window. The selected sample shows up above the image pane on the main screen (purple box, Figure 2). - On the main screen, select Objective, Filters, Light Source, Contrasting Method, and Illumination Method (orange boxes, Figure 2).
- Click on Acquire (yellow box, Figure 2) to bring up the image capture window, which shows the live image from the microscope. If you have a settings Profile (purple box, Figure 3) saved, be sure it is selected.
–You can adjust the image using the sliders under Gamma, Contrast, and Saturation (orange boxes, Figure 3).
–You can adjust exposure settings, image capture area, and focus area (green box, Figure 3; see Image Capture User Guide for details). *NOTE: You must use Full Chip as your Imaging Area or the scale bar will be incorrect. - When you are happy with your image, click Acquire (red box, Fig. 3). The image capture window closes after the image is acquired. The new image appears in the main window (Fig. 4) of the Image Capture program.
Figure 3. Image Capture software interface showing live image. Select the correct objective and Optovar (upright microscope) or magnification wheel (stereoscope) combination from the drop down list under Objective (orange boxes, Figure 2). The scale bar will be automatically calculated and added to the image by the software upon upload. If the settings on the microscope differ from those selected, the scale bar will be incorrect.
For a detailed explanation of how scale bars are added, see page Image Capture: Image Scaling_378P.- If you are happy with the image, click Upload (red box, Figure 4) to upload the image to the LIMS database.
Note: you can add comments (yellow box, Figure 4) such as species name or other pertinent information.
Figure 4. Image Capture software interface showing acquired image. - The image disappears after upload; however, you can get it back by clicking on the Objective drop-down menu. If you want to save a copy to a local folder, click on Export (green box, Figure 4).
Note: this only saves a copy of the jpeg image; a high-resolution tiff is saved in the database and can be accessed through LIMS Reports (LORE). - You can check to see if your image was saved in the LIMS database through LIMS Reports (LORE); however, you do not need to do this after every image capture.
Trouble shooting
If the SPOT warning message in Figure 5 is appearing in your software version, please go to Image Capture, click Acquire. Then click Prefs (Preferences) and change the Image Acquisition Bits per Channel to 8.
Figure 5. Image Capture warning message on Acquire-Acquire and related image of how to fix the error.
Credits
This document originated from Word document Image Capture QSG_v1.1.doc (see Archived Versions below for a pdf copy) that was written by D. Kulhanek (2013-05-28). Credits for subsequent changes to this document are given in the page history.
LIMS Component Table
| ANALYSIS | TABLE | NAME | ABOUT TEXT |
| MICROIMG | SAMPLE | Exp | Exp: expedition number |
| MICROIMG | SAMPLE | Site | Site: site number |
| MICROIMG | SAMPLE | Hole | Hole: hole number |
| MICROIMG | SAMPLE | Core | Core: core number |
| MICROIMG | SAMPLE | Type | Type: type indicates the coring tool used to recover the core (typical types are F, H, R, X). |
| MICROIMG | SAMPLE | Sect | Sect: section number |
| MICROIMG | SAMPLE | A/W | A/W: archive (A) or working (W) section half. |
| MICROIMG | SAMPLE | text_id | Text_ID: automatically generated database identifier for a sample, also carried on the printed labels. This identifier is guaranteed to be unique across all samples. |
| MICROIMG | SAMPLE | sample_number | Sample Number: automatically generated database identifier for a sample. This is the primary key of the SAMPLE table. |
| MICROIMG | SAMPLE | label_id | Label identifier: automatically generated, human readable name for a sample that is printed on labels. This name is not guaranteed unique across all samples. |
| MICROIMG | SAMPLE | sample_name | Sample name: short name that may be specified for a sample. You can use an advanced filter to narrow your search by this parameter. |
| MICROIMG | SAMPLE | x_sample_state | Sample state: Single-character identifier always set to "W" for samples; standards can vary. |
| MICROIMG | SAMPLE | x_project | Project: similar in scope to the expedition number, the difference being that the project is the current cruise, whereas expedition could refer to material/results obtained on previous cruises |
| MICROIMG | SAMPLE | x_capt_loc | Captured location: "captured location," this field is usually null and is unnecessary because any sample captured on the JR has a sample_number ending in 1, and GCR ending in 2 |
| MICROIMG | SAMPLE | location | Location: location that sample was taken; this field is usually null and is unnecessary because any sample captured on the JR has a sample_number ending in 1, and GCR ending in 2 |
| MICROIMG | SAMPLE | x_sampling_tool | Sampling tool: sampling tool used to take the sample (e.g., syringe, spatula) |
| MICROIMG | SAMPLE | changed_by | Changed by: username of account used to make a change to a sample record |
| MICROIMG | SAMPLE | changed_on | Changed on: date/time stamp for change made to a sample record |
| MICROIMG | SAMPLE | sample_type | Sample type: type of sample from a predefined list (e.g., HOLE, CORE, LIQ) |
| MICROIMG | SAMPLE | x_offset | Offset (m): top offset of sample from top of parent sample, expressed in meters. |
| MICROIMG | SAMPLE | x_offset_cm | Offset (cm): top offset of sample from top of parent sample, expressed in centimeters. This is a calculated field (offset, converted to cm) |
| MICROIMG | SAMPLE | x_bottom_offset_cm | Bottom offset (cm): bottom offset of sample from top of parent sample, expressed in centimeters. This is a calculated field (offset + length, converted to cm) |
| MICROIMG | SAMPLE | x_diameter | Diameter (cm): diameter of sample, usually applied only to CORE, SECT, SHLF, and WRND samples; however this field is null on both Exp. 390 and 393, so it is no longer populated by Sample Master |
| MICROIMG | SAMPLE | x_orig_len | Original length (m): field for the original length of a sample; not always (or reliably) populated |
| MICROIMG | SAMPLE | x_length | Length (m): field for the length of a sample [as entered upon creation] |
| MICROIMG | SAMPLE | x_length_cm | Length (cm): field for the length of a sample. This is a calculated field (length, converted to cm). |
| MICROIMG | SAMPLE | status | Status: single-character code for the current status of a sample (e.g., active, canceled) |
| MICROIMG | SAMPLE | old_status | Old status: single-character code for the previous status of a sample; used by the LIME program to restore a canceled sample |
| MICROIMG | SAMPLE | original_sample | Original sample: field tying a sample below the CORE level to its parent HOLE sample |
| MICROIMG | SAMPLE | parent_sample | Parent sample: the sample from which this sample was taken (e.g., for PWDR samples, this might be a SHLF or possibly another PWDR) |
| MICROIMG | SAMPLE | standard | Standard: T/F field to differentiate between samples (standard=F) and QAQC standards (standard=T) |
| MICROIMG | SAMPLE | login_by | Login by: username of account used to create the sample (can be the LIMS itself [e.g., SHLFs created when a SECT is created]) |
| MICROIMG | SAMPLE | login_date | Login date: creation date of the sample |
| MICROIMG | SAMPLE | legacy | Legacy flag: T/F indicator for when a sample is from a previous expedition and is locked/uneditable on this expedition |
| MICROIMG | TEST | test changed_on | TEST changed on: date/time stamp for a change to a test record. |
| MICROIMG | TEST | test status | TEST status: single-character code for the current status of a test (e.g., active, in process, canceled) |
| MICROIMG | TEST | test old_status | TEST old status: single-character code for the previous status of a test; used by the LIME program to restore a canceled test |
| MICROIMG | TEST | test test_number | TEST test number: automatically generated database identifier for a test record. This is the primary key of the TEST table. |
| MICROIMG | TEST | test date_received | TEST date received: date/time stamp for the creation of the test record. |
| MICROIMG | TEST | test instrument | TEST instrument [instrument group]: field that describes the instrument group (most often this applies to loggers with multiple sensors); often obscure (e.g., user_input) |
| MICROIMG | TEST | test analysis | TEST analysis: analysis code associated with this test (foreign key to the ANALYSIS table) |
| MICROIMG | TEST | test x_project | TEST project: similar in scope to the expedition number, the difference being that the project is the current cruise, whereas expedition could refer to material/results obtained on previous cruises |
| MICROIMG | TEST | test sample_number | TEST sample number: the sample_number of the sample to which this test record is attached; a foreign key to the SAMPLE table |
| MICROIMG | CALCULATED | Top depth CSF-A (m) | Top depth CSF-A (m): position of observation expressed relative to the top of the hole. |
| MICROIMG | CALCULATED | Bottom depth CSF-A (m) | Bottom depth CSF-A (m): position of observation expressed relative to the top of the hole. |
| MICROIMG | CALCULATED | Top depth CSF-B (m) | Top depth [other] (m): position of observation expressed relative to the top of the hole. The location is presented in a scale selected by the science party or the report user. |
| MICROIMG | CALCULATED | Bottom depth CSF-B (m) | Bottom depth [other] (m): position of observation expressed relative to the top of the hole. The location is presented in a scale selected by the science party or the report user. |
| MICROIMG | RESULT | adapter_tube | RESULT adapter tube: the adapter tube used on the microscope camera coupler to the microscope (e.g., D10ZNC or 60N-C coupler) |
| MICROIMG | RESULT | camera | RESULT camera: the type of camera used (e.g., SPOT, Axiocam) |
| MICROIMG | RESULT | contrasting_method | RESULT contrasting method: the type of microscope contrasting method (e.g., lightfield, darkfield, singly [or uncrossed] polarization, cross polarization) |
| MICROIMG | RESULT | field_of_view (mm) | RESULT field of view (mm): the field of view of the microscope as configured for this image (based on magnification and Optivar setting) |
| MICROIMG | RESULT | file_create_date | RESULT creation date: date/time stamp for the creation of the image file |
| MICROIMG | RESULT | filters | RESULT filters used: the filters that were in place when the image was taken (e.g., blue conversion filter 3200/5500 K, analyzer, polarizer) |
| MICROIMG | RESULT | illumination_type | RESULT illumination type: transmitted or reflected light |
| MICROIMG | RESULT | jpeg_image_asman_id link | RESULT JPG image ASMAN_ID: serial number of ASMAN link for the JPG/JPEG image |
| MICROIMG | RESULT | jpeg_image_filename | RESULT JPG image filename: filename of the JPG/JPEG image file |
| MICROIMG | RESULT | light_source | RESULT light source: light source used (e.g., halogen bulb 12V/100W, Zeiss microLED, VisiLED MC 1000) |
| MICROIMG | RESULT | objective | RESULT objective: type and magnfication of the objective used |
| MICROIMG | RESULT | tiff_image_asman_id link | RESULT TIF image ASMAN_ID: serial number of ASMAN link for the TIF/TIFF image |
| MICROIMG | RESULT | tiff_image_filename | RESULT TIF image filename: filename of the TIF/TIFF image file |
| MICROIMG | SAMPLE | sample description | SAMPLE comment: contents of the SAMPLE.description field, usually shown on reports as "Sample comments" |
| MICROIMG | TEST | test test_comment | TEST comment: contents of the TEST.comment field, usually shown on reports as "Test comments" |
| MICROIMG | RESULT | result comments | RESULT comment: contents of a result parameter with name = "comment," usually shown on reports as "Result comments" |
Archive Versions
- Image Capture Quick Start Guide.pdf: A PDF version of Image Capture QSG_v1.1.doc
- Image Capture Quick Start Guide - 24022020