In this brief study, we examine efficient methods for imaging entomology collections with the following aims:
- more than 5,000 specimens to image
- deciding the optimum quality and resolution possible
- low total cost per specimen
- handle a wide variety of specimen sizes
- 3 views per specimen (anterior, dorsal, lateral)
As a comparison, we’re using the current process at various entomology institutions as a baseline to compare low resolution and high resolution batch imaging processes using various tools available today.
Collection Policy Decisions
The key decision is weighing the tradeoff between the ultimate resolution and depth of field and a practical time to produce the image. Clearly as the resolution and focus depth increases, the time to photograph the images (and to a much lesser extent, to process) increases. It is key then to consider and decide the appropriate resolution for each section of, or for the whole, collection.
This decision is non-trivial as it is often tempting to get the collection viewable and online as soon as possible – a significant step forward from today’s inaccessible collections. However, the majority of the time and staff effort is in retrieving, preparing, and setting up the specimens for imaging and then returning them to storage. The actual photography is fully automated, as, to a lesser extent, is the processing which may require some manual intervention and decision making for optimum results. Given that, we believe that choosing a resolution for the automated photography part of the process is the critical decision. Once the photoset is captured, lower resolution images can be easily and quickly created.
We expect that image consumers (be they academics, visitors, web users, etc.) will demand, over time, better quality (that is sharper, more detailed, more accurate color, etc. images) and better tools, for example for annotation. The analog here is mapping, think of the resolution and information on web-based mapping systems ten years ago versus today. We believe that capture should be done once, and those original photographs stored with full metadata and detail, so that subsequent demands for improvements in quality, as above, can be met. We also believe that significant improvements in computing power, tools to process images and tools to extract detail in ways not yet available will all be applied to the captured photographs to produce new, and better, images.
Following the automated capture and storage, photographs can be rapidly processed for immediate inclusion in an online catalog, and over time higher resolution images can be added.
Batch Capture Containers and Setup
There are many methods for placing specimens and orienting them for the 3 distinct views in this example. Here we’ve chosen to use some inexpensive plastic containers to place the specimens, orient them for different views, and manage the process. We chose this method for the main reason that we can place each specimen once and then handle the plastic container to position the specimen on the imaging stage. We can also easily orient the container at the three different positions to be imaged (dorsal, lateral, and anterior). Many other options can be used an each institution’s may choose to use the method that works best for them.
General Assumptions
- Full-time staff member production over the course of a standard 8 hour day.
- Current process vs GIGAmacro process will result in equivalent (or better) results in terms of quality and resolution.
Current Typical Entomology Capture Process: 24 specimens per day / 20 minutes each
This process is based on the current imaging process in use at various scientific organizations for producing 3 views of entomology specimens. Each specimen is prepared, images captured, and post-processed as a single image stack. Average times reported are 3 specimens per hour (3 views each). An imaging technician is required during the entire process.
- Uses a commercial focus stacking system.
- Produces a focus stacked image (multiple images to gain a higher depth of field).
- Canon 21 megapixel camera with Canon MPE-65mm lens.
GIGAmacro Batch Capture Process: 80 specimens per day / 6 minutes each
In this process we photograph a group of specimens at a time using the GIGAmacro magnify2 robotic imaging system. The technician prepares the specimens for imaging and then starts the process. The system then runs automatically while the technician prepares other specimens or attends to other work.
- Uses GIGAmacro magnify2 system.
- Produces focus stacked images (multiple images to gain a higher depth of field).
- Canon 18 megapixel camera with Canon MPE-65mm lens with telecentric lens adapter.
- Uses one computer for image capture and one computer for automated post-processing.
GIGAmacro Batch Capture: High Resolution: 8 specimens per day / 1 hour each
- Uses GIGAmacro magnify2 system.
- Produces stacked and stitched images with increased depth of field and resolution.
- Canon 18 megapixel camera with Canon MPE-65mm lens with telecentric lens adapter.
- Uses one computer for image capture and one computer for automated post-processing.
GIGAmacro Batch Capture: High Resolution Optimized: 24 specimens per day / 20 minutes each
- As above, but uses an optimization routine to pre-calculate areas of each specimen that have detail to capture and bypass areas without information, such as the background area between a specimens wings.
- Process can reduce capture time by approximately 50%-80%.
- Process is currently in development with estimated completion later in 2014.
Additional Time Savings:
Additional time and efficiency can be gained by running the systems unattended overnight and/or at weekends. An additional 50% productivity improvement is anticipated.
Batch Capture Examples
Capture & Processing Time: < 6 minutes / specimen
Images Captured: 16-30 images captured per view
Example 1 Resolution: 6100 Pixels Per Inch (ppi)
Example 2 Resolution: 26,000 Pixels Per Inch (ppi)
Batch Capture High Resolution Example
Capture & Processing Time: avg 1 hour / specimen
Images Captured: 250-400 images captured per view
Example 1 Resolution: 25000 Pixels Per Inch (ppi)
Example 1 Resolution: 45000 Pixels Per Inch (ppi)
Gene is a creative innovator and developer with a passion for developing scientific tools, exhibits, and educational programs that provide new ways of exploring the world both literally and figuratively.
Photography is a common thread in his life and work, which has come a long way since childhood years experimenting with unique perspectives, angles, filters, and time-lapse exposures.
He founded GIGAmacro to build robotic devices capable of capturing gigapixel photographs with microscopic detail and developing new visualization tools for comparison of complex imagery for research, science, and education.
