Guide

Guide Contents

Digitising Your Reference Material

By Andrew Martin, University of Oxford· 3rd February, 2023

The Global Pollen Project aims to provide a home for digital pollen reference collections.

We provide tools for easy digitisation of reference collection slides. These have the following advantages:

  • Taxonomy. We provide a taxonomic backbone to verify taxonomic information, and provide quick data entry.
  • Focus Images. Images can be stacked and presented as focusable images, just like using a microscope.
  • Integration. Your slides will appear alongside slides from other collections, and user uploaded grains.
We are working on providing DOIs and archival downloads of digitised pollen collections in the next release. Please contact us for more information.

The Digitisation Process

Digitisation is completed using the online Digitisation Dashboard.

Starting the Collection

For a reference collection, we require a collection name, a basic description, curation details, and access details. How you organise slides into reference collection sets is up to you.

Recording a Slide

The only requirement for recording a reference slide is a taxonomic identification. There are three types of identification supported for reference material:

  1. Direct. The pollen or spore sample was taken directly from a plant, which has been identified.

  2. Morphological. The pollen or spore was identified to a family, genus, or species based on its morphology only.

  3. Environmental. A pollen sample was taken from the contemporary environment. A morphological identification was performed. The choice of possible taxa was constrained by species occurrence lists at the space and time at which the pollen or spore was found.

For material with a direct identification, we ask for more information about the method through which the plant was identified. The following options are provided:

Botanical ID Method Description Required Optional
Herbarium Voucher The sample was taken directly from a herbarium voucher, which was professional identified within a herbarium. Herbarium Code, Herbarium's internal ID for this voucher N/A
Living Collection in a Botanic Garden The sample was taken directly from a living plant within a recognised botanic garden. Botanic garden code, and the botanic garden's internal ID for this particular plant. N/A
Field Identification A living plant was identified in situ. N/A The forenames and last name of the person who identified this plant.

Note that we currently do not accept reference material where the taxonomic system used is morphological pollen types. This feature is planned for a future release: if you would like to use this feature, let us know.

Aside from the taxonomic identity and associated data, additional metadata may be provided about the provenance of the sample:

Data Description Options
Existing ID Code If you have already catalogued your slides using ID numbers or codes, these can be translated into the Global Pollen Project. Short Text
Location The location from which the sample was initially taken. For example for herbarium vouchers, this is the location of plant harvest. For environmentally-derived pollen samples, this may be the location of a pollen trap or sediment coring location. Continent; Country; Locality; or Unknown
Year of Collection For directly identified material, or environmental samples, you may specify the year of collection. Calendar Year

Finally, we encourage full information to be provided about the manufacture of the palynological slide itself. This data is again optional:

Data Description Options
Prepped By The first names or initials, and last name of the person who created the slide from any sample or residue. Person; or Unknown
Prep Date The year in which the slide was manufactured. Calendar Year
Chemical Processing The most destructive procedure that has been applied to the sample. Please select 'fresh grains' for material that has not been chemically processed. Fresh Grains; Acetolysis; HF; or Unknown
Mounting Medium The mountant used to fix the pollen or spores to the slide. Silicone Oil; Glycerol; or Unknown

When your slide is submitted, its identity within our taxonomic backbone will be calculated based on the identification provided. Please refer to documentation on the taxonomic backbone for more information.

Uploading Images

You can upload as many images as necessary to an individual slide. To enable dynamic scalebars on images, and future use of the dataset for pollen / spore traits, every image must be calibrated to micrometre space.

To achieve this, there are two image options available: static and focus images.

Static images can be taken ad-hoc, for example using a smartphone camera looking down an eyepiece. A 'click-click' calibration is completed using a known measured distance on the image itself. Static images are approprate for slides that have previously had images taken to varying scales and image dimensions.

Focus images require a fixed-camera setup on your microscope. The fixed-camera and microscope combination is calibrated using a calibration set (seel below). When uploading a focus image, you are presented with a drop-down choice of microscope and, if a compound microscope is used, the magnification levels that have been calibrated.

'Fully Digitised' Status

A reference slide becomes 'fully digitised' when:

  1. The taxonomic identity provided is valid within our taxonomic backbone;
  2. The taxonomic identity of the slide gains 'confirmed' status; AND
  3. There is at least one static or focus image uploaded.

Reference slides can be published without being fully digitised, but they will not appear in the Global Pollen Project's master reference collection.

Publication

You must request publication of a reference collection for it to be made public. Your collection will now enter content review. This process is not designed to be a 'gatekeeper' to material contributed, but to validate that no obscene images or language, or mistakes, have been entered. There are two decisions that may be made:

  • Accepted. The collection will be published immediately as an individual reference collection. Any fully digitised slides will be incorporated into the Global Pollen Project's Master Reference Collection.
  • Revision Required. We may advise that changes are made, if errors, corrupt images, or invalid content are detected. You will recieve a note with changes requested. Once these are complete, you can request publication again.

Publication is irreversable: any errors must be corrected by issuing a new version of your reference collection.

Microscope Calibration

To support focus images, microscopes may be calibrated using images of a scale bar at each magnification level. The key requirement for this is that your microscope is set up with a fixed camera that does not move.

The digitisation tools include a 'click-click' measurement to save the measurement of a scale bar image as pixel units in the image.

For a compound microscope, you must configure the magnification of the ocular lens and objectives. You may then calibrate each objective individually, allowing images to be submitted at varying magnification levels from a single microscope.

The digitisation tools also support digital microscopes that only have a single fixed magnification.

Crediting Contributions

The Global Pollen Project contains tracking of contributions within reference collections. The information captured for each slide includes:

  • If field-based plant identification was conducted, who the identifier was
  • Who collected the pollen residue used to create the slide
  • Who prepared the slide
  • Who 'digitised' the slide (i.e. uploaded it to the GPP)

We use this information to compute appropriate references for reference collection material that is both digitised and undigitised.

Curation of Reference Material

Content review is conducted by a small team of Global Pollen Project curators, who attempt to complete this within one to two days.

Collection Versioning

Collection versioning ensures that historic versions of reference material are always available, for example when referenced from an academic paper.

The GPP's master reference collection will always reflect the most recent published versions of reference material.

Ready to add your own reference material?

Start the digitisation process.