Setting up Camera

Body

1)      Set Mode Dial to M (Manual) **Make sure the lens set to Manual Focus, and the dial on the top of the camera is set to “M”

a)      Quality: set to Raw (this gives full resolution images in raw Canon format)

b)      Set Custom WB according to manual – using off=white card

c)      Set Standard picture style

Lens

1)      Set to MF mode (Manual Focus)

2)      Make sure lenses are fully locked

Setup

1)      Attach metal pole from camera stand into tripod groove on camera (safest way to do this is by screwing it into the camera before attaching camera to stand)

2)      Attach metal pole back to camera stand and adjust as horizontally as possible (use level stick and make sure bubble is in the center)

3)      Plug white cord USB into computer and into camera digital terminal

4)      Open Helicon Remote.

Shooting images in Helicon Remote

Camera settings:

1)      The exposure mode should be set to Manual, and greyed out.

2)      Set the Time: This is the shutter speed setting. It controls how long, in seconds, the shutter will be open. The longer the shutter is open, the more light hits the sensor and the faster the shutter closes the darker the image. Play around with this setting until you find a good exposure, THEN STEP IT DOWN 1 OR 2 POSITIONS. Images lighten as they ‘stack’, so starting low ensures no nasty surprises.

3)      Choose an Aperture: Aperture determines how wide the focal range is. A rule of thumb here is: the lower the number, the smaller the slice. This setting will also influence brightness, so adjust the exposure time if you need to. While it is tempting to crank it all the way down to 2.8 for everything, realize sometimes thicker ‘slices’ with overlapping focus slices can help eliminate blurry area.

4)      Set the ISO: ISO for our purposes stays between 100 and 250. This reduces the speckling that can be seen in images with long exposures and high ISO’s.

5)      Ev is greyed out, but it stands for Exposure value.

6)      Select a Quality: Output file types are set here. Normally, JPEG is fine as long as it is the ‘Fine Large’ JPEG. These can be converted to TIFFS in the post processing.

Below this is the Histogram. For specimen photography, this is not the most useful. It can be used to see the effect of the polarizing filter on the heavy peaks in the white zone (the right hand side).

Specimen Setup:

All images must have a scale bar. The color bar is optional, but highly recommended, it is very useful during post-processing. Background should be black velvet, brown velvet or white cardstock. Specimens should be well lit, with no opaque shadows and no ‘hot spots’ of overexposed areas. If this is not possible, err on the side of too dark, as you can always lighten an image but you cannot restore detail where overexposure has obscured it.

1)      Find the lowest point of relief on the specimen. The scale bar laid beside the specimen is a very good proxy for this point.

2)      In the live view window, click this spot.

3)      Using the arrows above the A and B buttons to get this area in focus.

4)      Once you are happy with the focal plane, click the B button. A lock will appear.        

At this point, you may NO LONGER TOUCH THE LENS.

Changing the focus after one of the focus brackets has been set will result in out of focus images.

5)      Click anywhere in the live view window to see the whole image again.

6)      Find the highest point, and click on it.

7)      Using the arrows, get this area in focus.

8)      Click on the A button.   

9)      ‘Shots’ counts the number of pictures that will be shot between the A and B focal planes. The drop down next to this should be set to infinity. Ensure that the interval is set to one.

1. 1. 1. If you select the auto DOF then the number of shots and their interval is selected for you.

10)   There are 2 checkboxes at the bottom of this section.

1. 1. 1. DOF preview you get a view of your near and far points, so you can verify that they are OK.
      2. Selecting Highlight focused areas will cause the in focus pixels to highlight in blue.
         
         
                                                          

11)   Exposure bracket is the next section, but we don’t use it. If you were doing HDR photography, this would be where you set your exposures.

12)   The Advanced Settings section lets you adjust white balance and temperature.

1. 1. Change white balance to fluorescent if just ambient light in room.

13)   Choose Color Temperature if you want custom control.

1. 1. Higher numbers give a yellow/orange tint
   2. Lower numbers give a blue tint

14)   Hit the Start shooting icon.

15)   When the lens stops moving hit Helicon Focus button.

Helicon Focus (HF)

1)      The images from Helicon Remote will populate into the image selection panel.

2)      Right click the first image, and choose ‘select all’.

3)      Select “Run” from the top of the right window, and wait for the program to finish

4)      Save as high quality JPG (setting 12) or TIFF. Remember to use the file naming convention outlined in previous document.

5)      Hit file tab to return to the stack, delete the selected images for this last run and then selected those for the next render.

Tips for good stack series:

1)    Use brush to gently dust off any dirt on specimen.  Finish with the hand-pumped air blower.

1. 1. Open the image file ‘fragile_specimen_space_holder’ in the procedures folder under NSF images on the server. Type in the specimen number, and save a copy to the processed images folder. Use the same file naming protocol for this place holder as you would a normal image. This assures that when the images get published to the web, people who look for the specimen know it's not imaged, but it is here.
   2. In the inventory tracking file, make a note that the specimen is too fragile to handle

Positions

1)    A good rule-of-thumb is to take about 3 views per specimen, although this number will vary with individual differences.  In general, it is good to take dorsal (top), ventral (bottom), and lateral (side) views, and any others that will capture important detail.  For example, if photographing an echinoid, take the standard dorsal, ventral, and lateral views.  Then you should also take a fourth view of the aboral end (opposite of the oral end).

Photography: 

1)    Any given drawer will most likely have specimens with a range of sizes, colors, and shapes.  You can minimize the number of lens and exposure changes if you group the specimens by size and color before photographing.

2)    The limiting factor when you are photographing small specimens with lens extenders is vibration of the camera body, caused anytime you touch the camera or lights, and also by the shutter.  Let the camera settle for a few seconds after focusing and after taking each picture.  For close work, don’t use exposures longer than 1/15 second (this may require using smaller f-stops).

HeliconFocus:

1)      When combining images, HF works best when the image slices in the selection list are in the correct order and same orientation.  We recommend focusing first on the scale bar for the first shot, and then moving upwards toward the specimen.  If they are not, the blending may not work.  This is usually a problem when the image numbers are greater than 9.  This can be corrected by loading the images in two stages, as shown in the example below.

2)      In some cases when you have multiple focal planes the final combined image is bad.  Sometimes this can be corrected by eliminating one of the focal plane images and then recombining.

3)      An undocumented feature of HF is that it writes to a cache file and never erases it.  Over time, this cache can get quite large and you should erase it manually every week or so.  The file is located on the C: drive in the Documents and Settings directory.  The path will depend on your user id. Look for the cache in:

C:\Documents and Settings\<userid>\Local Settings\Application Data\Helicon\Focus4\cache

Erase any subdirectories you find in the cache directory.