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Home > Resources > Digital Imaging Process for Database Images

 

Capturing and Processing Digital Images of Plant Specimens
In the University of North Carolina Herbarium
by Stephen Seiberling

System Description

Overall Description

The system for capturing images of herbarium specimens in the University of North Carolina at Chapel Hill Herbarium employs a high resolution digital camera mounted on a copy stand with an attached lighting system. The camera chosen for the project is suited to producing large images that preserve a high degree of detail and color accuracy. The copy stand and lighting system permit one to readily control and reproduce particular lighting conditions, providing consistency in image quality over time.

The ProgRes 3012 camera used on the project is a professional digital camera scanner manufactured by Kontron Elektronik GmbH, with a Lametar 2.8/25mm. lens. The camera is capable of capturing images at resolutions of up to 4,608 x 3,480 pixels, and generating 12 bits per color channel. Control of the camera is provided through a program that functions as a plugin for Adobe Photoshop. The software currently runs on an IBM-compatible Dell Pentium II PC with a special PRI-PCI interface board that attaches the computer to the camera through a 50-pole data cable. After capture, images are manipulated in Adobe Photoshop 5.5, saved in both compressed and uncompressed formats, and archived on recordable compact discs.

The Bogen System 800 copy stand includes four 250 watt halogen lamps mounted in pairs on two adjustable support arms, enabling one to position the lamps at differing heights and angles relative to the surface of the copy stand table. Lighting intensity can be adjusted using a graduated dimmer control box. The height of the camera above the copy stand table is altered using a motorized height control mechanism, which permits fine adjustments in camera position. A ruled guide built into the stand's camera support column is useful for referencing different configurations of the system.

Lighting Setup

Proper illumination of herbarium specimens is critical for producing high quality images using the ProgRes 3012 camera. Bright, direct lighting is helpful for accurate color rendition and preserving certain types of detail. However, we have found that direct lighting can produce confusing shadows in images of herbarium sheets that have a three dimensional element. This is especially problematic when the light striking the object is coming from more than one direction. Diffused lighting, by contrast, is useful for minimizing shadows, but tends to produce a softening effect and a loss of sense of depth for three dimensional objects, and can lack sufficient brightness for the camera to reproduce color accurately.

The best lighting setup for capturing good quality images that we have developed to date involves a combination of diffused and direct light, coming from one general direction. The two lighting support arms attached to the copy stand table are positioned so that the pair of lamps on the lower arm shines directly on the portion of the table where specimens are placed for imaging. These lights are positioned out to one side at a low angle (about 35 degrees) relative to the surface of the table. The upper lighting support arm is positioned on same side of the table as the lower arm, but at an angle of about 70 degrees relative to the table surface. The pair of lamps on the upper support arm is aimed at a the upper half of a white foam core board panel (30" x 20" x 3/16") positioned on the side opposite the lights. None of the light from these upper lamps strikes the specimen directly, but instead is reflected off the panel onto the specimen. Thus a shadow is cast on one side of objects due to the low angle of the direct lighting, which is then softened by the reflected light bouncing of the white panel. The reflected light also helps to produce more even illumination across the surface of the table.


The lighting configuration, and procedures described below, reflect the results of informal experimentation with the ProgRes 3012 camera over the course of several months. Helpful advice was provided by Gene Hammond of Catalist, Inc. in Greensboro, NC, Steve Davis of the UNC Chapel Hill Anthropology Dept., and Gregory Georges. Information contained in the ProgRes Plugin user's manual (Release 3.x, June 1996), was also used in developing these instructions.


Capturing Images

Preparing Herbarium Specimens for Imaging

An annotation label should be attached to each herbarium sheet prior to imaging. Labels for the North Carolina Botanical Information Network (BOTNET) or Plant Information Center (PIC) projects should include the name and international abbreviation of the UNC Herbarium, the BOTNET name, the taxonomic name being assigned to the particular specimen, the name of the person responsible for the taxonomic determination and imaging of the specimen, and the date when the specimen is imaged. For example:

Herbarium of the University of North Carolina (NCU)
Specimen image captured for the
North Carolina Botanical Information Network (BOTNET)
Acer barbatum Michx.
Det. & imaged by: Stephen M. Seiberling February , 2001

The precise day of the month may be written in by hand just prior to imaging. The label should be printed on cotton fiber paper and glued to the sheet in a location where it does not cover other annotations or any part of the specimen itself.

A University of North Carolina Herbarium bar code label should also be added to the herbarium sheet. When possible attach the bar code label to the lower left-hand corner of the sheet. Otherwise look for another spot along the lower edge of the sheet, or in some other unobtrusive location.

It can be helpful, prior to imaging, to place the set of specimen sheets in an order consistent with how the resulting image files will be numbered. (See File Naming Convention under Manipulating and Saving Images in Photoshop below, for more details.) For the PIC project, within each taxon, images representing examples of leaves are numbered first, followed by examples of flowers, and lastly, examples of fruits.


Checking the Lighting and Physical Setup of the Camera

Make sure the lamps on the lower lighting support arm are positioned to shine directly on the area of the table where specimens are to be placed for imaging. The upper pair of lights should be aimed at the white reflection panel on the opposite side, so that direct light from them strikes the upper part of the panel and not the specimen itself. Lighting intensity when capturing images, as indicated on the Varilight 2000 control box, should be set to 10 to provide maximum illumination. (The halogen bulbs in the lamps have a relatively short life, so it's best to leave them off except when necessary to setup and capture images.)

Check the height of the camera relative to the surface of the table. A standard sized herbarium sheet can be fully captured when the camera is set to a height of 126 cm. as indicated by the position of the lower edge of the motorized height control mechanism on the ruled portion of the copy stand column. If necessary adjust the camera height using the Varispeed 1000 control device.

Verify that the plane of the camera's light sensors is parallel to the table surface using the bubble level. The bubble should come to rest in the same position when placed against the downward facing, front edge of the camera body, as it does when placed on the glass surface of the copy stand table. If there is a discrepancy, gently rotate the camera body by hand in the appropriate direction, and check again using the bubble level.

Unscrew the lens cap and place it where it won't get lost. (Remember to replace the lens cap when done.)

Capturing Images with the ProgRes Camera

Step 1. Turn on the camera using the green switch on the camera's power supply box.

Step 2. Open Adobe Photoshop. Select File>Import>ProgRes_v.4.01 to open the ProgRes camera plugin software.

Step 3. Click on the Configure... button in the ProgRes Plugin main window. The selected Colour Matrix file should be ps_reflect1.mtx. (See Color Calibration in Calibrating the ProgRes 3012 Digital Camera for information about creating color matrix files for specific lighting setups.) The following features in the Configuration window should be marked with a check:
Colour Balance
Gradation Curves
Shading Correction: White and Black
Sharpen Image should not be marked with a check. Focal Length should be 25 mm., Image Resolution 300 dpi, Units Pixel, Photoshop Export RGB, and Colour 0-255. (If any of these setting have been altered, they may be reestablished by clicking on the Load... button in the Configuration window, selecting the config1.con file, and clicking the Open button.) Once all settings have been set correctly in the Configuration window click on Ok to exit.

Step 4. Click on the Balance... button in the ProgRes Plugin window. Click Load..., select the bal1.tac file and click Open. This will reload the color balance values to those previously established for the standard lighting conditions. Click Ok to exit the Colour Balance window. (If these settings produce unsatisfactory results see Setting Shadow and Highlight Color Balance Values in Calibrating the ProgRes 3012 Digital Camera.)

Step 5. Make sure the Image Format in the ProgRes Plugin window is set to 1497*1160 Pixel, and that the Overexposure box is checked. Check that the Exposure time, as indicated in the lower left portion of the plugin window, is set to 1 and not some higher number.

Step 6. Place the herbarium sheet on the copy stand table with the large piece of heavy white paper underneath it. Make sure that the entire sheet is visible in the ProgRes Plugin display window. (For oversized specimens it may be necessary to increase the height of the camera above the table.) Turn on the four copy stand lamps, if they are not on already, by first pressing the power switch on the Varilight 2000 control box and then rotating the dimmer knob to 10. Turn off the room overhead lights and the lights in the adjacent room (if the door is open). Adjust the aperture ring on the camera lens so that all of the "false" green color just disappears. (The false green indicates areas that are overexposed and will lack detail in the resulting image.)

Step 7. Temporarily remove the herbarium sheet from the copy stand and place the focusing device (see below) on the table more or less centered under the camera.

Image

Click on the Start Focus button, and adjust the lens focal ring until the image is sharply focused as indicated by the height of the vertical green bar on the right side of the plugin window, or the number just to the right of the Stop Focus button. Maximum height of the green bar and highest numbers indicate sharpest focus. Note that the position of the focus area may be changed using the slider bars below and to the right of the display window. (If the focus bar appears to jump erratically, making it difficult to focus precisely, double check the Exposure time to verify that it is set to 1. Also make sure your fingers are away from the front of the lens, and take care to avoid exerting pressure on the side of the camera or lens when focusing.) Click on the Stop Focus button when done.

Step 8. Remove the focusing device and reposition the herbarium sheet on the copy stand table Adjust the position of the sheet so that it is fully visible and centered in the plugin display window. Make sure that each edge of the sheet is parallel to the adjacent side of the display window. It's helpful to set the display window to 200% in order to check the position carefully. Place a scaling device in an appropriate location on the herbarium sheet. Readjust the aperture if necessary to eliminate any areas of overexposure.

Step 9. Click on Capture to scan the specimen. Avoid altering the lights or otherwise interfering with the camera while scanning is in process. (Once the small window says "Assembling...", it's safe to remove the sheet from the table.) When image capture is complete, a new window will open in Photoshop displaying the results of the scan. You may wish to expand the image display size to 100% using the Zoom Tool in order to make sure that sharpness and color are acceptable before saving the file.

Once the above steps have been carried out to successfully capture an initial image, it is relatively easy to quickly scan a number of herbarium sheets since lighting, camera height, image resolution, focus, etc. have been checked or properly set. After the first sheet has been scanned, save it as a TIFF file (see Step 5 under Preparing Archival Image (TIFF) Files, below), before rotating, cropping or otherwise adjusting the image. Then scan a series of sheets in succession without changing the lighting, focus or other settings, appropriately naming (see File Naming Convention, below) and saving each in turn. After a desired number of images have been captured, turn off the copy stand lights and the camera power supply, replace the lens cap, restore the normal room lighting, and manipulate each image as described below.


Manipulating and Saving Images in Photoshop

Once an image has been captured with the ProgRes 3012 camera it needs to be manipulated in order to produce files suitable for archiving, displaying on the internet and/or sending by email.

Preparing Archival Image (TIFF) Files

Step 1. With the newly scanned image visible in a Photoshop window, select Image>Rotate Canvas, and then choose either 90° CW (clockwise) or 90° CCW (counter-clockwise) as needed to properly orient the herbarium sheet on the monitor. (An entire folder of images may be rotated automatically by selecting File>Automate>Batch and choosing the BOTNET Image Manipulation Set, and the Rotate 90 CW or the Rotate 90 CCW Action. The appropriate Source and Destination folders must be chosen in the Batch window.)

Step 2. Images captured with the ProgRes camera typically require sharpening to make details in the image fully visible. The following procedure seems to produce better results than using the sharpening function contained in the ProgRes plugin software. With the new image visible in Photoshop, maximize the image window and increase the image size to 100%. Select Filter>Sharpen>Unsharp Mask... from the menu bar. The following settings produce good results for previously unsharpened images taken as described under Capturing Images with the ProgRes Camera above:
Amount 200%,
Radius 0.8 pixels,
Threshold 2 levels.
Click on OK to perform the sharpen procedure. (This procedure can be run on an entire folder of images by selecting File>Automate>Batch and choosing the BOTNET Image Manipulation Set, and the Unsharp 200, 0.8, 2 Action. The appropriate Source and Destination folders must be chosen.) Since image sharpening causes a loss of data, it is best to avoid applying extreme sharpening procedures to the archival version (TIFF) of the file. The above settings produce a moderate degree of sharpening that introduces minimal distortion in the image.

Step 3. With the image window maximized, zoom in or out using the Zoom Tool until the image is displayed at 66.7%, as indicated at the top of the window. (The Zoom Tool is contained in the Photoshop Toolbox, which can be displayed by selecting Window>Show Tools from the menu bar.) Next select the Crop Tool, located with the Marquee Tool, in the uppermost left portion of the Toolbox. Click and drag with the left mouse button starting from one of the upper corners of the herbarium sheet down to the opposite corner. This creates a rectangular selection area that will be used to cut out parts of the image. (It's not necessary to make the Crop box fit precisely at this point since it can be resized before cropping.) Rotate the Crop selection area, if needed to make the edges of the box line up as parallel as possible to the sides of the sheet in the image. To do this, position the mouse outside the box and move the mouse with the left button depressed. (Some sheets aren't perfectly rectangular, so you must simply find a good compromise.) Change the size of the selection area by clicking and dragging the small squares at the corners or on the sides of the box as needed. Leave about a quarter inch (as seen at 66.7% of full size) of the background on the left and right sides. Leave as much room as you can at the top and bottom, while being sure to eliminate the colored band of distortion that appears at one end. Again check both the top and bottom of the sheet to be sure the selection area is well aligned. Press enter, or double click inside the selection area to crop the image. (If you make a mistake select Edit>Undo Crop from the menu bar, and try cropping again.)

Step 4. Increase the image display size to 100%, and evaluate the need for adjustment of color levels by selecting Image>Adjust>Levels (or pressing CTRL?L). If there is no data at the leftmost or rightmost ends of the graphical display of the image output range, reduce the Output Levels to compensate for this. To do this, slide the pointer at the left end of the graph to the right so that it lines up with the leftmost edge of the data. Do the same with the pointer on the right end, moving it leftward, if there is no data that extends to the rightmost edge of the graph. Now adjust the pointer in the middle of the graph sliding it left or right to establish the optimum middle tone in the image. It is helpful to refer to the actual specimen when adjusting the middle tone in order to produce a level of brightness and contrast in the image that most faithfully preserves it's appearance. Once you're satisfied with the color levels click OK. It is also often helpful to adjust the brightness and contrast of the image by selecting Image>Adjust>Brightness/Contrast Try adjusting the contrast of the image in order to more accurately reproduce the range of contrast in the actual specimen. If needed, alter the image brightness also. Again, compare the image to the specimen during this procedure to recreate its actual appearance as closely as possible. Altering brightness and contrast can produce subtle distortion in the image, especially in text areas, so its best to apply these adjustments with moderation. Adjusting Levels and Brightness/Contrast appropriately is something of a skill that improves with experience.

Step 5. Save the file now by selecting File>Save As..., and choosing the TIFF (*.TIF) format in the popup window. Give the file an appropriate name, including the .tif extension (see File Naming Convention below). Click the Save button. Select IBM PC for the Byte Order in the TIFF Options window and click OK. The resulting file will be just under five MB in size, assuming the image was captured using the 1497*1160 Pixel resolution.

Preparing Files for Web Display or Emailing

This procedure assumes that the image has already been captured, processed, and saved as a TIFF file using the steps described above under Preparing Archival Image (TIFF) Files.

Step 1. Open the appropriate TIFF file if it is not currently displayed in Photoshop.

Step 2. Some images appear to benefit from additional sharpening beyond that resulting from the procedures described above. To do this, first increase image size to 100%, and select Filter>Sharpen>Unsharp Mask... from the menu bar. Good settings to use to bring out detail, while introducing minimal distortion, in images that have been processed as above are:
Amount 90%,
Radius 0.3 pixels,
Threshold 2 levels.
Click on OK to perform the sharpen procedure. It may be necessary to experiment some with the settings to determine the best result. Be careful to not to save the sharpened image as a TIFF file at this point.

Step 3. Select File>Save As... from the menu bar, and choose the JPEG (*.JPG, *.JPE) format in the Save As window. Choose the appropriate subdirectory and file name (see File Naming Convention below for PIC project images), and click on the Save button. In the JPEG Options window set the Image Options Quality to 8. (This setting determines the degree of compression that will be applied to the file. A setting a of 8 maintains relatively high image quality, while still significantly reducing the file size.) Choose Baseline Optimized under Format Options to preserve the highest color quality of the image. After clicking OK Photoshop modifies the image and saves it in JPEG format. The size of the file should now be reduced to about 150 to 350 KB, depending on the complexity of the image.

All of the procedures described above for creating JPEG images may be run automatically by selecting File>Automate>Batch then choosing the BOTNET Image Manipulation Set and selecting the Run F5 (Unsharp), F6 (JPEG) Action. The Source folder should be the directory where the appropriate TIFF files are located. The Destination folder is the location where the new files will be created. Be careful when choosing the Destination folder since the procedure creates files with the same name as source files, only with the extension changed to .jpg. Existing JPEG files will be overwritten if their names are the same as those being created. Note that the procedure operates on all image files located in the Source folder.

To the send an image by email, simply attach it to your email document as you would any other file. The recipient may view the file by using either a web browser or any of several image editing programs such as Adobe Photoshop.

Creating Thumbnail Images

Each JPEG file that is created for the BOTNET PIC project should have a corresponding thumbnail image.

Step 1. Start with the appropriate TIFF version of the image, which should be opened if it is not already displayed in Photoshop.

Step 2. Select Image>Image Size Make sure Constrain Proportions and Resample Image are checked in the Image Size popup window. The image resampling method should be set to Bicubic which produces more precise results with smoother tonal gradations. For PIC project thumbnail images, type in 104 pixels for the image Width under Pixel Dimensions. The height in pixels is automatically adjusted to maintain the existing proportions of the image. Click OK. Photoshop resamples the data and displays a reduced size image. (Be careful to not save the image using the existing TIFF file name and extension at this point.)

Step 3. It is often helpful to sharpen the thumbnail image files. The sharpening procedure is best applied before conversion to JPEG format. Select Filter>Sharpen>Unsharp Mask... from the menu bar. Good settings for sharpening thumbnail images are:
Amount 175%,
Radius 0.5 pixels,
Threshold 2 levels.
Click on OK to perform the sharpen procedure. Again be careful to not save the sharpened image using the original TIFF file name and extension.

Step 3. Select File>Save As... from the menu bar, and choose the JPEG (*.JPG, *.JPE) format in the Save As window. Choose the appropriate subdirectory and file name (see File Naming Convention below for PIC project images), and click on the Save button. In the JPEG Options window set the Image Options Quality to 8 and choose Baseline Optimized under Format Options to maintain good image clarity and color. The resulting file should be between 10 and 15 KB in size.

All of the above procedures for creating thumbnail images may be run automatically by selecting File>Automate>Batch then choosing the BOTNET Image Manipulation Set and selecting the Thumbnails 104 pix; unsharp 175 Action. The Source folder should be the directory where the appropriate TIFF files are located. Be careful when choosing the Destination folder since the automated procedure creates files with the same name as source files, but with the extension changed to .jpg. This will overwrite any full-sized JPEG images located in the Destination directory if they have the same name. Also note that the procedure operates on all TIFF or JPEG files located in the Source folder. For the PIC project it is necessary to manually edit the file name of each of the resulting thumbnail images, adding the "-t" tag (see File Naming Convention below), after running the batch procedure.

File Naming Convention

It is important to follow a standard procedure for naming files to ensure that each image has a unique name that is readily recognizable. All new BOTNET PIC project image files should now be named using the convention described below.

File names for images of herbarium sheets, or portions thereof, have three or four sections, depending on the type of image:

prefix - seq # - tag - .ext

prefix - consists of the genus and specific epithet of the specimen, connected by an underscore. In cases of infraspecific taxa, add a three-letter abbreviation of the infraspecific rank followed by the first three letters of the subspecies or varietal name, both connected with underscores. Use the scientific name assigned to the particular taxon for the BOTNET PIC project, if different from that given on other herbarium sheet labels.

seq # - a three digit sequence number distinguishing images of specimens of the same species. Thumbnail images and detail images of portions of herbarium sheets have the same sequence number as the original, full sized image of the same specimen.

tag - indicates a thumbnail version (t), or a detail image of a portion of the specimen such as, cone (con) flower (flw), fruit (frt), label (lab), etc.; up to three characters. No tag is assigned to original specimen sheet images.

.ext - a three character extension for the image file type: i.e., .tif, .jpg, .gif, etc.

Examples:

Acer_barbatum004.tif - the original image (TIFF) file of a particular herbarium specimen of Acer barbatum Michx.

Acer_barbatum004-t.jpg - a JPEG thumbnail of the same specimen image of Acer barbatum Michx. as above.

Acer_barbatum004-frt.tif - a detail image of a fruit from the same specimen of Acer barbatum Michx. as above.

Acer_saccharum_var_sac001.jpg - a jpeg version of an herbarium specimen image of Acer saccharum Marshall var. saccharum.


Currently, the first numbers assigned to herbarium sheet images for a particular taxon for the PIC project are for those specimens representing examples of leaf forms, followed by those for flowers, and then those for fruits. (Note that the number of specimens providing examples of leaves, flowers or fruits may vary for different taxa.) For example:

Acer_barbatum001.jpg - an example of a typical leaf form for Acer barbatum Michx.

Acer_barbatum002.jpg - an alternative example of leaf form.

Acer_barbatum003.jpg - an example of flowers.

Acer_barbatum004.jpg - an example of fruits.


Images derived from illustrations or from photographs of live specimens should be named using a modified form of the above convention. For these images the four sections of the file name are rearranged in the following order:

prefix - tag - seq # - .ext

prefix - consists of the genus, specific epithet and any infraspecific information, as described above.
tag - indicates the type of special image such as photograph (pht) or illustration (ill), etc.; up to three characters.
seq # - a two digit sequence number distinguishing different photos or illustrations of the same species.
.ext - a three character extension for the image file type: i.e., .tif, .jpg, .gif, etc.

Example:

Acer_barbatum-ill01.jpg - a JPEG image of an illustration of Acer barbatum Michx.


Backing Up and Archiving Image Files

Creating Initial Backups of Image Files

Finished TIFF and JPEG image files should be saved in folders, or subdirectories, on the PC's hard drive. For the PIC project, new files should be stored in the Angiosperm Trees folder under the appropriate family and genus. For example, images of Acer barbatum Michx. would be saved in the C:\Angiosperm Trees\Aceraceae\Acer subdirectory. (Only the full-sized JPEG and TIFF files, and not the small thumbnail images, need be saved in the Angiosperm Trees folders.) Saving files in this ways facilitates creating well organized archival copies of the images on CD-R. To reduce the risk of losing images in the event of problems with the camera PC, once imaging for a genus or family is complete, copy the TIFF and full-sized JPEG files to the Angiosperm Trees folder on the Biology network server located in the \\Biodata\Staff\Herbarium\botnet subdirectory. For additional security, new files and their folders may then be copied from the network drive to the Angiosperm Trees folder on the C: drive of the other PIC-project PC located in the camera room.

Archiving Image Files on CD-R discs

Once TIFF and JPEG files have been created for a large number of images, a backup or archival copy on CD-R media should be made. In order to minimize excess use of CDs, wait until close to 650 MB of new image files have been saved on the computer's hard drive. Files should be transferred to CD as completed families whenever possible. Simply copy the folder for the entire family using the Easy CD Creator software, with the images contained in the appropriate genus subdirectories. Save as many completed families as will fit on the CD-R.

After copying files to CD-R, check for copying errors using the CDCheck software. The best method to use for this is to have the program's Compare function compare the original files and folders on the PC's hard drive to those written to the CD. If any files are corrupted, the process of copying images to the CD-R should be repeated using a new disc.

After copying and checking the files, write the name of the CD, e.g. Angiosperm Trees #1, on the label side of the CD itself using a water-based permanent marker. (Avoid using Sharpies, or other solvent-based markers, since these can cause damage to the CD resulting in data loss.) Also write the name of the CD, along with a brief description, including a list of the families represented, on the CD insert. For example,

TIFF and JPEG images of whole herbarium sheets for PIC project angiosperm trees:
Aceraceae
Anacardiaceae
Annonaceae
Apocynaceae
Aquifoliaceae
Araliaceae
Arecaceae
Asteraceae

A second copy of each CD-R should be prepared on a different brand of media for long-term archiving, since the actual longevity of CD-R discs is not well established and may vary from one type to another. Be sure to check the second CD for copying errors using the CDCheck software, as described above. CD-R brands that have been identified as more likely to be chemically stable over long periods of time include Mitsui Gold and Kodak Ultima.

 

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