Digital Photography & the Microscope
Introduction to Digital Photography and Microscopy
Some Factors Involved in Obtaining and Using Good Photomicrographs
The Digital Image Formation Chain
Selection of Digital Cameras
Camera mounts
Camera Settings
Automatic Settings
Image print size
Manual setting mode
Focusing tips for Digital Cameras
Take some test photos
Getting your photos from camera to the computer
Simple method - flash card
Manufacturer's cables
Video bus
Building and Organizing a Digital Photo Library on a computer
Photo library management
Photo Library design
First Pass Screening
Saccardo Method
Image Library Backup Suggestions
References for Digital Photography
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Digital Photograph Database Design, Organization, Maintenance Suggestions
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Here we recommend designs for a database of digital photographs with focus on technical microphotography used to form a forensic particle identification data system - at low cost with easy to use tools. Discussion focuses on selection of cameras adapt well to microscope eyepieces or trinocular heads, and on camera settings and procedures to obtain best quality photographs. I also discuss image resolution and size settings and make recommendations. Cameras used as examples in this paper include the Nikon Coolpix series 990, 995, and 4500. The techniques discussed in this paper work well with digital cameras and any type of microscope, low power stereo zoom to high power forensic polarized light microscopes.] © Copyright 2009 Daniel Friedman, All Rights Reserved. Information Accuracy & Bias Pledge is at below-left. Use links at the left of each page to navigate this document or to view other topics at this website. Green links show where you are in our document or website. PAAA 2005 Symposium, University of Tulsa, Tulsa Oklahoma -
June 2-5, 2005 |
Organizing and finding digital micro-photographs on a computer
Selection of a photo library management program for Digital Photography through the Microscope
Library design is critical if a large number of photographs are to be stored and ever found again. we have found that general purpose PC-type software such as the Thumbs Plus photo management software by Cerious (www.cerious.com) is particularly suited for this purpose for these reasons which also will describe what we consider important in photo library software:
- The program permits ready directory creation, image movement, copying, and deletion without hogging disk space by keeping multiple copies of each image every time one is moved or changed. [The Mac iPhoto program is the world's worst offender in this regard.]
- Basic image manipulation such as rotation, cropping, enlarging, jpeg cleanup, image enhancement, color balance, saturation, contrast, brightness, are readily at hand.
- Image file naming and image clean up or manipulation functions can be applied either to individual photo images or can be applied to groups of pictures. This makes the assignment of meaningful names to images a snap as it can be done en masse rather than having to type in individual photo names.
- Directories can be scanned for duplicate or similar images
- A watermark can be assigned to images, e.g. for © protection
- Annotations and keywords can be assigned to each image, recording technical or descriptive data for each photo.
- Data base functions are provided, permitting searching for images based on name, assigned keywords, or annotations.
Library design for digital photographs through the microscope
Build a file or disk directory library of folders which organize your photos according to your reference library schema. Example, if you're an aerobiologist, mold, or pollen specialist, create folders for:
Microscopy Pictures - a sample library organization
- to be sorted - this is a general import photo directory
- Bacteria
- Ascomycota
- Yeasts
- Amphisphaeria
- Apiosporina
- etc
- Basidiomycota
- Uredinales RUST
- Ustilaginales SMUT MILDEWS
- Acryia
- Agaricales
- Agaricosa
- etc
- Myxomycota
- Mitospores
- Algae
- Chrytidomata
- Oomycota
- Zygomycota
- Pollen
- Animals, Fibers, Insects, Other
- Unknown Particles
First Pass Screening Microscopic Photo Collection by Family or Type
Using a schema similar to the above, we place one or two representative photos of each spore of a general class (Ascomycetes) in the root directory Ascomata and then place all of the additional reference photos of each Genera/Species within its own subdirectory. On recognizing a spore as an Ascomycete, we can quickly scan through my Ascomycete library of representative photos, pick candidates, and look at more photos in their detailed subdirectories where there will be photos of more spore variations and details.
Saccardo organization for Mold Spore Photographs
we have experimented with forcing my higher level reference directory photos into a Saccardo schema, particularly under the Mitospore category, but it's been tough to maintain this order. Scrolling through the library is so fast that it's easy enough to spot and scan, for example, hyaline allantospores that we stopped forcing those photos into a false order and just order them by their individual names.
Using annotations, keywords, and data base search. we include keywords, annotations, comments, with each photo to assist in identification, such as remarks from reference sources about distinguishing characteristics, habitat, etc. I find the annotations extremely helpful, the keywords and search functions we use very little in my lab.
Typical photo annotations include:
- Photo source
- Unique identifying features to look for
- Other similar spores or pollen grains to cross-check against
- Habitat information
- Reference text citation
- Pathogenicity
Let me know how you succeed, or if you're having trouble obtaining successful, sharp photos with good exposure, email me a photo or two. Sometimes by looking at a bad photo we can figure out what camera or microscope changes might improve results.
We are working on a visual spore and pollen key, and currently have about 250,000 images on hand, but still I'm lacking many of the common spores and pollen grains. Anyone willing to collaborate should send me a note.
Image file backups on trips
In the lab we make daily backups of my image library onto a second or even third device. One of these is portable and is carried home each night so that we have off-site backup data. Once the volume of images becomes substantial, use of a portable hard drive is more practical than writing CD's or DVD's.
We also carry an external hard drive on critical excursions, so that we can back up my photos in at least two different media/physical devices. With a laptop along one can also write a CD or DVD for non-volatile storage as well.
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Digital Photography & the Microscope
Introduction to Digital Photography and Microscopy
Some Factors Involved in Obtaining and Using Good Photomicrographs
The Digital Image Formation Chain
Selection of Digital Cameras
Camera mounts
Camera Settings
Automatic Settings
Image print size
Manual setting mode
Focusing tips for Digital Cameras
Take some test photos
Getting your photos from camera to the computer
Simple method - flash card
Manufacturer's cables
Video bus
Building and Organizing a Digital Photo Library on a computer
Photo library management
Photo Library design
First Pass Screening
Saccardo Method
Image Library Backup Suggestions
References for Digital Photography
References for Digital Photography Through the Microscope - Micro Photography
A Short Course in Nikon Coolpix 990 Photography, Dennis P. Curtain, http://www.shortcourses.com - RECOMMENDED
Resolution of Digital Photomicrographs from Scanned Film, Theodore M. Clark, Microscopy Today, Feb/Mar 2001 http://www.couger.com/microscope/Ted-Clarke/papers/FilmScanner/
Light, Michael I. Sobel, University of Chicago Press, 1987, ISBN 0-226-76751-5
ThumbsPlus image software, provides highly functional image database including basic editing, cropping, enlarging, enhancement of photos, image organization, keywords and comments attached to each image, and search capability - HIGHLY RECOMMENDED for PC platforms. Typically less than $100. Network support available.
PhotoShop image editing software, provides sophisticated image editing, available for PC and Macintosh computer platforms. Not recommended for reference library use - this is overkill for image editing and lacks good database functions. Typically more than $400.
iPhoto image software, provides easy user interface and limited function to organize and print photos for MAC computer platforms - not recommended, limited function, very wasteful of disk space, lacks good database functions. Free included with new Apple computers or operating systems.
Photo Explosion image software - free from Microsoft with other OS purchases. Untried.
Picture Easy software from Kodak - free with some Kodak cameras, simple organizing and photo manipulation.
Nikon View software - free from Nikon with purchase of Coolpix cameras, easy image import and simple image manipulation and printing. Great for printing contact sheets of photos (which themselves are pretty useless).
[1] Thumbs Plus image data base software from Cerious software, www.cerious.com is a top choice low-cost option), and will be searched-through for reference purposes
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