Image Capture Quick Start Guide


Introduction

This document provides an introduction to using the SPOT cameras and Image Capture software used on the JOIDES Resolution.  

Procedures

  1. 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.


  2. Open Image Capture software on computer and login with username, password, and expedition number.



    Figure 2. Image Capture software interface.


  3. 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).


  4. On the main screen, select Objective, Filters, Light Source, Contrasting Method, and Illumination Method (orange boxes, Figure 2).


  5. 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.


  6. 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.


  7. 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.


  8. 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.


  9. 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).


  10. 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

 

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