Imaging

SCAN IMAGING GUIDELINES for using Visionary Digital Equipment

Taking the image (BK Plus System)

 

Editing the image

 

Naming and saving the image

 

Post Processing

 

Batch Uploading

 

 Specimens are chosen to represent a species or morphospecies based on their curation and overall condition.  

TAKING THE IMAGE (BK Plus System)

  1. Turn on Camera.
    1. Note what aperture (F#) is set to (8.0 or 5.6 for 100mm lens and 5.6 for 65 mm lens, typically) (see screen on camera). 
  2. Open CamLift Controller.
    1. Click on the "Set Up Lens" button to set lense specifications according to your current setup.  
    2. Open up “Live View” to view image.
    3. Use up and down arrow keys in CamLift to move lift up or down.
    4. Step size adjustment (black rectangle on bottom third of lift): adjust for how much you want the lift to move.  For very large distances, infinite is good.  For smaller distances, move to different increment (usually start with 2mm or 1mm, depending on lens/camera)
  3. Turn on Dynalite lighting system by pressing power button.
    1. To make image lighter or darker, press full, quarter, or half button to adjust. For each lamp, they don’t have to be both set at quarter-quarter, half-half, etc, but you can. For finer adjustment, turn Power Variation knob clockwise for less light intensity (make sure to dump stored light by pressing Read/Test botton).  For more light intensity, turn counter clockwise.  When increasing light intensity, there is no need to dump light. 
  4. Situate specimen
    1. For dorsal: specimen should be facing left :
       
    2. For lateral: specimen should be facing to the left. 
  5. Get specimen in focus by dragging lift down.
    1. To adjust specimen size in image, adjust zoom on camera lens.  (100 mm – 1:1  is greatest mag., 65mm – 5X is greatest mag.). 
  6. Get image roughly in focus for a test shot.
    1. CLOSE OUT OF LIVE VIEW FIRST BEFORE TAKING PICTURE. Not doing so puts unnecessary mechanical strain on the camera and will ultimately shorten its lifetime.
    2. Open Lightroom and your picture will open in LightRoom.
    3. If the picture comes out to bright or dark return to Step 3 (if you take a picture and it doesn’t go to Lightroom, go to settings > Save Pictures folder > Click on “LR Watch”).
    4. After making the necessary adjustments you can begin stacking the image.
  7. Find highest point of specimen, zoom in on live view (the magnifying glass in the lower left hand corner of the live view window) and focus to that point (a 1x step size would help here), then click “Start Here.”
    1. Follow the same steps for the lowest point of specimen and click “Stop Here.”
    2. Before clicking start in Autorun, make sure there are no images are in LightRoom.  
  8. Now click “Autorun” (Live View will automatically close out).
    1. In Autorun, select current lens setting. For example, pick 100mm 1x if you are using the 100mm lens and the magnification is at 1x.
    2. Click Start in CamLift to begin slice imaging.

LightRoom

This program can be used to make simple edits to white-blance, color tone, and as well as image meta-data. In general most users can simply use the histogram found in the top right corner to examine the overall quality of their image. Most people aim to achieve a large amount of the histogram's data in the middle, which illustrates a good balance between color and lighting. If necessary (the histogram is skewed right or left) then you can make simple adjustments under quick develop on the right-hand side. 
For more information try: Lightroom Tutorials

  1. Once you are done making any necessary modifications, highlight all your slices and click File>Export to rename and export your images.
  2. In Export Window:
    1. Export to: Specific Folder (ie Pieridae_GEWA22444)
    2. Create Subfolder (ie Dorsal or Lateral)
    3. Save filename:  Project/Catalogue #_lens mm_ focus (Ie GEWA22444_100mm_1to1)
    4. Save slices  in Primary Image Drive

Helicon Focus

  1. Begin by opening the folder where you have save all of your images through File> Add New Items> "Folder".
    Open images: Navigate to the folder in which your image slices are saved.
  2. When you have navigated to the folder containing all of your image slices for the current specimen, and no other images are present in that folder, click “Run” (in the upper right hand corner).
  3. Helicon will now stack your image and an output file will be produced.
    1. If your output image has a "halo" or blurred edges trying first modifying the Radius default, and if artifacts still persist than try the Smoothing default.
    2. To learn more about the effects of both Radius and Smoothing, as well as stacking perimeters, try: Understanding The Focus Stacking Parameters.
  4. After the stacking is finished, save the final file as a TIFF in the same folder as your image slices.

EDITING THE IMAGE

Photoshop

  1. Now open the Photoshop and click: File > Open > "File Name"

  2. To Sharpen: Filter > Sharpen > Smart Sharpen (Usually, keep between 20 and 35, although it depends on the image and personal preference).
     
  3. To make Scalebar:
    1. Select>Image > Analysis > Set Measurement Scale> Click on your corresponding lens  (ie 100mm) and magnification (ie 1:1) for your image. If you are unsure, it should be in the image’s filename.
    2. Now select:  Analysis: Place Scale marker (make font bigger, between 30 and 72)
    3. Make any necessary adjustments to font and place the scale in the BOTTOM RIGHT CORNER. 
    4. To drag: click select tool (Uppermost tool in side toolbar, above crop tool)

NAMING AND SAVING THE IMAGE

  1. Save the finished image (Save As) in Primary Image Drive using the following format: UID_ASPECT. 

    Examples:

    NAUF4A1234567_D for a dorsal view
    NAUF4A1234567_L for a lateral view
     
  2. If you have two images of the same aspect a suffix must be added: NAUF4A1234567_D_a.tiff, NAUF4A1234567_D_b.tiff, etc.
  3. Place your final image (named as UID_ASPECT) in the following directory: X:\SCAN Symbiota Images\SAVE_TIF_HERE ("X:\" refers to the CPBC_Imagery network share drive, this will vary from person to person).
  4. If you would like to keep an original for you own security or otherwise, please save a copy of the original .TIF/.TIFF in a separate location.

POST PROCESSING

These steps take advantage of the actions option in Photoshop. We have created a scripts and a set of actions which anyone can download and modify according to their specifications: Post-Processing and Add File NameFor "Add File Name" please copy and paste text into a '.txt' file.

If you would like to learn more try about either process, try: How To Save, Share, Download and Photoshop Actions and Introduction to Photoshop Scripting

If you'd like to learn about our system folder set-up please whatch our Folder Setup Guide.

*Please move our AddFilenamePlus.js script to your Photoshop script folder (i.e. C:\Program Files\Adobe\Adobe Photoshop CS6 (64 Bit)\Presets\Scripts) before begininning this process. 

  1. Open Photoshop
  2. Click Window>Actions (this will open a window allowing you to create, load, and implimant batch action scripts)
  3. In Action window select dropdown menu at the top right-hand corner (should be right below the "x"; first option will say "Button Mode")
  4. In dropdown menu select "Load Actions..."
  5. Find the downloaded action file from above: "Post-Processing.atn"
  6. You have now have a new action available for your use and modification on Photoshop. 
  7. For batch post-processing:
    1. Select File>Scripts>Image Processor…
      1. Select Folder “SAVE_TIF_HERE” (CPBC_Imagery\SCAN Symbiota Images\SAVE_TIF_HERE)
      2. Select Folder “Processed_Tif_Jpeg” (CPBC_Imagery\SCAN Symbiota Images\DO_NOT_TOUCH\Processed_Tif_Jpeg)
      3. Make sure “Save as JPEG” box is checked
        1. Make sure “Save as TIFF” box is checked
      4. Check Run Action
        1. In FIRST dropdown box select “Default Actions”
        2. In SECOND dropdown box select “Post-Processing”
      5. Step 5
        1. Click Run
  8. Photoshop will now batch process your images and Save the files to the “Processed_Tif_Jpeg” folder.

BATCH UPLOADING

  1. Become a NAU research affiliate
    1. Fill out the NAU Affiliate form and return it to Paul.heinrich@nau.edu.
    2. One you are added as an affiliate (you will receive an email) you will need to call NAU Information Technology Services at 928-523-1511 to get your userid and password.
    3. Contact Paul Heinrich with your new NAU user id and he will give you rights to connect to the share.
  2. Connect to the NAU domain via VPN
    1. See http://nau.edu/its/services/vpn/ for details on how to create a VPN connection of Mac, PC or Linux systems.  You will need to disconnect from any existing VPN before you connect to the NAU VPN.
    2. It is important to use the form NAU\userid for your userid when you VPN into NAU.
    3. Email Paul.heinrich@nau.edu if you have problems.
  3. Connect to the SCANBUGS samba share at NAU
    1. For PCS you need to use “Map Network Drive”
      1. Right click “My Computer” and choose “Map Network Drive”
      2. Use any free drive letter.
      3. Use \\jan.ucc.nau.edu\scanbugs\incoming\ as the folder.
    2. For Macs you need to use “connect to server”.
      1. Open a folder window.
      2. Click on the “Go” menu.
      3. Type the server address smb://jan.ucc.nau.edu/scanbugs/incoming
      4. Click connect.
  4. Navigate to your collection folder (we used the collection code from the scan repository for the folder names)
  5. Copy your image files to the folders
    1. Be sure that the file names for image files include the object id for the specimen in the image and saved in JPG/JPEG format.
  6. Wait overnight for the server scripts to link your images to the SCAN database
  7. By the next morning, you should see your images linked to the proper collection specimen