Methods & Protocols

To ensure scientific utility and long-term archival value, the IFML adheres to strict digitization protocols. Our methodology prioritizes resolution, color accuracy, and non-destructive handling of specimens.

Digitization Hardware

All specimens are digitized using large-format, high-resolution flatbed scanners, specifically the Epson Expression 13000XL. This hardware was selected for its ability to capture exceptionally fine details across a large scan area, crucial for larger compound leaves and twig specimens.

Scanning Parameters

• Optical Resolution: Minimum of 1200 DPI (dots per inch).
• Color Depth: 48-bit color (16 bits per channel). This ensures a wide color gamut and captures subtle variations in leaf chlorosis, pubescence, and bark texture that would be lost in standard 24-bit scans.
• File Format (Raw): Uncompressed TIFF.

Image Processing & Curation

Following the raw scan, images undergo a standardized post-processing workflow to maximize their utility for diverse applications.

Tier 1: Archival Package (Research Use)

This package contains the raw, unprocessed 48-bit TIFF files. These files are enormous and are intended for scientific analysis where data integrity is paramount (e.g., algorithmic venation analysis, color spectroscopy simulation).

Tier 2: Access Package (General Use)

These images are derived from the raw scans but have been processed for easier handling. Backgrounds are digitally removed to create transparent PNGs, and files are downsampled slightly (though still maintaining 4K+ resolution) for easier integration into presentations, educational materials, and web design.

1. Pre-Scan Calibration
   Verify scanner warm-up time (minimum 30 minutes). Perform color calibration check using ColorChecker target. Document ambient temperature and humidity.
2. Specimen Positioning
   Place specimen on scanner bed with adaxial (upper) surface facing down. Include metric ruler or scale bar in frame. Ensure specimen lies completely flat with no curled edges.
3. Scanner Settings Configuration
   Set resolution to 1200 DPI optical (no interpolation). Select 48-bit color depth. Disable automatic color correction and sharpening. Set output color space to Adobe RGB.
4. Initial Scan Execution
   Perform full-resolution scan. Save as uncompressed TIFF with embedded color profile. Generate MD5 checksum immediately after saving.
5. Quality Control Inspection
   Verify image sharpness at 100% zoom. Check for dust, artifacts, or color casts. Confirm scale bar is readable and in-focus. Re-scan if quality issues detected.
6. Metadata Documentation
   Record: Species (scientific and common names), collection date, location (GPS coordinates), collector name, phenological stage, specimen dimensions, pixels-per-millimeter calculation.
7. Web Preview Generation
   Convert TIFF to PNG at 1200 DPI for web display. Apply sRGB color space conversion. Compress PNG with lossless optimization. Maintain original aspect ratio.
8. File Organization
   Use naming convention: [Genus]_[species]_[SpecimenType]_[YYYYMMDD]_[UniqueID].tif
   Example: Quercus_bicolor_Leaf_20260106_001.tif
   Download Naming Standards (PDF)

Scale Verification & Morphometrics

Archival Storage & Zenodo Upload

1. Pre-Upload Validation
   Run TIFF Validator to confirm: 48-bit depth, uncompressed format, embedded color profile, minimum 1200 DPI, file integrity via checksum.
2. Metadata JSON Creation
   Generate standardized JSON file with Dublin Core fields: Title, Creator, Subject (species), Description, Date, Type (Dataset/Image), Format (image/tiff), Rights (CC BY 4.0).
3. Zenodo Community Upload
   Upload to IFML Archive community. Include both TIFF (master) and PNG (preview). Attach metadata JSON. Assign keywords: "Forestry", "Iowa", "Dendrology", scientific name.
4. DOI Assignment & Verification
   Publish record to receive permanent DOI. Verify DOI resolves correctly. Update collection tracking spreadsheet with status: "Published".

Citation of Methodology

Researchers using these protocols should cite as follows: