Digital Photograph Database Design, Organization, Maintenance Suggestions

Photo image data bases for micro-photography: how to organize and use an efficient and full-function database of digital photographs
MICROSCOPE DIGITAL PHOTOGRAPHY - How to take photographs through the microscope
Selection of Digital Cameras
Camera Settings
Focusing tips for Digital Cameras
Getting your photos from camera to the computer
Building and Organizing a Digital Photo Library on a computer
References for Digital Photography
Questions & Answers about digital photograph database methods to store and retrieve a large library of images using simple computer software
References

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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.

Organizing and finding digital micro-photographs on a computer

Abstract: How to build a database of photographs for computer access, sorting and management. 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.]

PAAA 2005 Symposium, University of Tulsa, Tulsa Oklahoma - June 2-5, 2005
Note: the latest version of this document can be found at InspectAPedia.comhttp://InspectAPedia.com/mold/digipix.htm
last update 20 August 2007 © Daniel Friedman All Rights Reserved

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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Technical Reviewers & References

Related Topics, found near the top of this page suggest articles closely related to this one.

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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Environmental Health & Investigation Bibliography - our technical library on indoor air quality inspection, testing, laboratory procedures, forensic microscopy, etc.
Adkins and Adkins Dictionary of Roman Religion discusses Robigus, the Roman god of crop protection and the legendary progenitor of wheat rust fungus.
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"A Brief Guide to Mold, Moisture, and Your Home", U.S. Environmental Protection Agency US EPA - includes basic advice for building owners, occupants, and mold cleanup operations. See http://www.epa.gov/mold/moldguide.htm
US EPA - Mold Remediation in Schools and Commercial Building [Copy on file at /sickhouse/EPA_Mold_Remediation_in_Schools.pdf ] - US EPA
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Fungi, Identifying Filamentous, A Clinical Laboratory Handbook, Guy St-
US EPA: Mold Remediation in Schools and Commercial Building [Copy on file at /sickhouse/EPA_Mold_Remediation_in_Schools.pdf ] - US EPA
Mycology, Fundamentals of Diagnostic, Fran Fisher, Norma B. Cook, W.B. Saunders Co. 1998, ISBN 0-7216-5006-6 (buy this book at Amazon)
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