1 | P a g e HERBARIUM DIGITIZATION PROCESS MANUAL
2 | P a g e HERBARIUM DIGITIZATION PROCESS MANUAL
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4 | P a g e HERBARIUM DIGITIZATION PROCESS MANUAL Introduction A Digital Herbarium is a systematically organized repository of digitized herbarium specimens, high-resolution images, and associated metadata. It functions as a digital archive for the preservation, management, and dissemination of botanical collections. Herbarium digitization involves the creation of high-quality digital images of preserved plant specimens together with the capture of essential specimen information, including scientific name, family, collector's name, collection date, collection locality, accession number, and other relevant metadata. The digitization process minimizes physical handling of specimens, thereby reducing the risk of damage while supporting their long-term preservation. A digital herbarium provides efficient access to botanical collections through electronic storage, indexing, searching, and retrieval of specimen records. It supports taxonomic studies, biodiversity documentation, ecological research, conservation planning, and educational activities by enabling convenient access to authenticated specimen data. The establishment of a digital herbarium ensures the long-term preservation of botanical heritage, improves collection management, facilitates data sharing and scientific collaboration, and enhances the availability of plant specimen information for research, education, and biodiversity conservation.
5 | P a g e HERBARIUM DIGITIZATION PROCESS MANUAL HERBARIUM SCANNING Digitization of preserved herbarium specimens using a high-resolution herbarium scanner to create archival- quality digital images along with specimen metadata for long-term preservation, research, and online access.
6 | P a g e HERBARIUM DIGITIZATION PROCESS MANUAL RAW SAMPLE SCANNING Digital imaging of raw drug samples and medicinal plant materials for documentation, quality assurance, authentication, reference collection development, and database creation.
7 | P a g e HERBARIUM DIGITIZATION PROCESS MANUAL OBJECT SCANNING Object scanning is the process of capturing high-resolution digital images of plant parts, crude drugs, seeds, fruits, leaves, flowers, stems, roots, bark, and other botanical specimens using a dedicated object scanner. The purpose is to record detailed morphological characteristics for scientific documentation, identification, research, digital archiving, and educational applications.
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10 | P a g e HERBARIUM DIGITIZATION PROCESS MANUAL Objectives • Preserve herbarium specimens digitally • Provide rapid access to specimen information • Reduce physical handling of specimens • Create a searchable image archive • Support scientific research and documentation
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12 | P a g e HERBARIUM DIGITIZATION PROCESS MANUAL Start-up Procedure START COMPUTER SYSTEM AND HERBARIUM SCANNER Herbarium Scanning P
13 | P a g e HERBARIUM DIGITIZATION PROCESS MANUAL Herbarium Scanning Procedure (Parameters) Two different scanning configurations were adopted to meet both routine access. Long-term archival and high- quality digitization of the Herbarium. 1. Standard Access Copy Color Mode: 24-bit RGB Resolution: 300 dpi File Format: JPEG The initial scanning configuration employed 24-bit RGB color mode, 300 dpi resolution, and the JPEG file format. This combination was selected to achieve an optimal balance between image quality and file size, ensuring clear visual representation while minimizing storage requirements. The resulting images are well suited for routine documentation, digital access, and efficient online distribution. 2. Archival Master Copy Color Mode: 48-bit RGB Resolution: 600 dpi File Format: TIFF This configuration was chosen to create a preservation-quality master image with the highest possible level of color accuracy and fine detail. The combination of 48-bit color depth, 600 dpi resolution, and the lossless TIFF format ensures that the digital image retains maximum visual information, making it suitable for scientific documentation, detailed analysis, future image processing, and long-term archival preservation. Copy Type Purpose Color Mode Resolution File Format Recommended Use 1. Standard Access Copy For viewing, web display, database access, printing, and sharing 24-bit RGB 300 dpi JPEG (High Quality, Smaller file size, fast loading, suitable for everyday use 2. Archival Master Copy Long-term digital preservation and future reprocessing 48-bit RGB (16-bit per channel) 600 dpi TIFF Uncompressed Highest image quality with no compression loss; suitable for archival storage
14 | P a g e HERBARIUM DIGITIZATION PROCESS MANUAL Technical Details for Images Processing Microsoft ScanWizard Graph The toolbar contains the following buttons: Button Function Overview Captures a low-resolution preview of the entire scanner bed. Prescan Generates a detailed preview of the selected area before final scanning. Zoom Tool Enlarges the image for detailed inspection. Hand Tool Moves the image within the preview window. Scan Starts the final high- resolution scan. RAW Enables RAW image capture for maximum image quality. Preview Area (Centre Window) The large central area displays the herbarium sheet placed on the scanner. The specimen includes: • Pressed plant specimen • Herbarium label • Colour calibration chart • Measurement scale • Collection number tag Type: RGB Colors The specimen is scanned in full color mode. Red Dotted Rectangle The red dotted boundary represents the: Scan Frame (Scanning Area) Only the material inside this frame will be scanned and saved. Users can: • Resize the frame • Move the frame • Crop unwanted margins
15 | P a g e HERBARIUM DIGITIZATION PROCESS MANUAL Technical Details for Images Processing Resolution (Res): 600 dpi The image is scanned at 600 dpi, which is recommended for herbarium digitization because it provides: • High detail • Long-term archival quality • Accurate morphological observations Image Size Estimated output file size depends of selected dpi of images. Higher resolution produces larger files. Scanner Profile ObjectScan 1600 CCSG This profile ensures: • Proper color management • Accurate image reproduction • Standardized scanning conditions Auto Corrections Automatic image enhancements can be applied, including: • Brightness adjustment • Contrast correction • Color balancing • Typical Workflow Shown in the Image • Place herbarium sheet on scanner bed. • Click Overview. • Adjust the red scan frame. • Set scan resolution to 600 dpi. • Verify color mode (RGB). • Click Prescan. • Check image quality. • Click Scan. • Save image in TIFF/JPEG format. Images Size The approximate file size of an A3-sized image scanned at 600 dpi depends on the color mode and file format. For a paper size of 29 cm × 42 cm scanned at 600 DPI, the pixel dimensions are: Dimension Calculation Pixels Width (29 ÷ 2.54) × 600 6,850 pixels Height (42 ÷ 2.54) × 600 9,921 pixels Pixel Dimensions at 600 DPI 29 cm × 42 cm = approximately 6850 × 9921 pixels Note: The standard A3 paper size is actually 29.7 cm × 42 cm. Using the standard A3 dimensions: Width: (29.7 ÷ 2.54) × 600 = 7,016 pixels Height: (42 ÷ 2.54) × 600 = 9,921 pixels Standard A3 at 600 DPI = 7016 × 9921 pixels. Approximate File Sizes Color Mode TIFF Uncompressed JPEG (High Quality) Grayscale (8-bit) ~66 MB 8–15 MB RGB Color (24- bit) ~199 MB 20–50 MB For Herbarium Digitization Most institutions scan herbarium sheets in: • RGB Color • 600 dpi • TIFF format
16 | P a g e HERBARIUM DIGITIZATION PROCESS MANUAL Technical Details for Images Processing For an A3 herbarium sheet of 29 cm × 42 cm scanned at 300 DPI in 24-bit RGB colour mode, the pixel dimensions are: Using 29 cm × 42 cm Parameter Value Paper Size 29 cm × 42 cm Resolution 300 DPI Colour Mode 24-bit RGB (8 bits × 3 channels) Width in Pixels 3,425 pixels Height in Pixels 4,961 pixels Pixel Dimensions: 3425 × 4961 pixels Calculation • Width: (29 ÷ 2.54) × 300 = 3,425 pixels • Height: (42 ÷ 2.54) × 300 = 4,961 pixels If using the official ISO A3 size (29.7 cm × 42.0 cm) Parameter Value Paper Size 29.7 cm × 42.0 cm Resolution 300 DPI Width in Pixels 3,508 pixels Height in Pixels 4,961 pixels Standard A3 (ISO 216) at 300 DPI = 3508 × 4961 pixels Approximate File Sizes (3508 × 4961 pixels) Colour Mode Uncompressed TIFF JPEG (High Quality) 24-bit RGB ≈ 49.8 MB ≈ 5–10 MB For your Herbarium Scanning (Digitization) Process Manual, you can use the following specifications: Image Type Colour Mode Resolution Pixel Dimensions File Format Standard Access Copy 24-bit RGB 300 DPI 3508 × 4961 pixels (A3) JPEG Archival Master Copy 48-bit RGB 600 DPI 7016 × 9921 pixels (A3) TIFF
17 | P a g e HERBARIUM DIGITIZATION PROCESS MANUAL Image Saving and Data Management Proper image saving and data management are essential for maintaining a reliable and accessible digital herbarium repository. Saving Scanned Images After successful scanning, save the digital image in the designated storage directory using standardized file naming conventions. Recommended File Formats: Master Archival Copy: TIFF (.tif) format at 600 dpi Access/Reference Copy: JPEG (.jpg) format at 300 dpi Each scanned specimen should be assigned a unique file name to ensure easy retrieval and avoid duplication. Recommended Format: Collection Number Botanical Name_Date.tif Collection Number Botanical Name_Date.jpg Example: 0104_Holoptelea_integrifolia_2022-09-07.tif 0104_Holoptelea_integrifolia_2022-09-07.jpg Directory Structure Scanned images should be organized systematically within folders based on family, collection year, or accession number or any ID number. Specimen Metadata The metadata for each herbarium specimen should be systematically recorded in a structured database along with its unique RRDR Code/barcode number. The recorded information including the following details : 1. Collection Number 2. Botanical Name 3. Family 4. Common/Local Name 5. Collector Name 6. Date of Collection 7. Place of Collection 8. GPS Coordinates 9. Habitat Information 10. Phenological Status 11. Digital Image Reference The metadata associated with each specimen serves as an essential source of scientific information for researchers and collector. It supports accurate taxonomic identification, facilitates studies on geographic distribution and biodiversity, preserves the historical record of specimen collection, and enables efficient management of herbarium collections. The unique barcode assigned to each specimen provides a permanent identifier, ensuring accurate tracking, easy retrieval, and seamless integration with digital herbarium databases and biodiversity information systems. Following image acquisition, specimen information should be entered into the herbarium database.
18 | P a g e HERBARIUM DIGITIZATION PROCESS MANUAL Herbarium Specimen Metadata Recording The metadata of each herbarium specimen shall be recorded in a standardized tabular format to ensure uniformity, traceability, and efficient digital data management. The information recorded for every specimen will include the RRDR Code/Barcode Number, Field/Collection Number, Scientific (Botanical) Name, Family Name, Collector's Name, Place of Collection, Date of Collection, and the name of the person responsible for digitization. This metadata will facilitate accurate indexing, retrieval, verification, and long-term preservation of herbarium records within the digital repository. Herbarium Specimen Metadata Register Annexure 1 S NO RRDR CODE/ BARCODE FIELD NO. SCIENTIFIC NAME FAMILY COLLECTED BY PLACE OF COLLECTION DATE OF COLLECTION DIGITIZED BY 01 RRDRGP0001 F-001/2025 Ocimum tenuiflorum L. Solanaceae Dr. A.K. Sharma Haridwar, Uttarakhand 5-10-2025 R. Kumar
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21 | P a g e HERBARIUM DIGITIZATION PROCESS MANUAL Quality Control Guidelines
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