CALIFORNIA PHENOLOGY
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Document Library

For webinar recordings, visit our webinars page.
For quarterly reports, visit our reporting page.
​See the bottom of the page for meeting recordings.

Resource Name
Description
Date Published / Last Updated

Associating Barcode Numbers with Accession Numbers Protocol (Step 5)
​This protocol describes how to link specimen images to their existing records in CCH2 by transcribing the accession numbers on the images. This step is necessary for institutions that had records in CCH2 before imaging and did not update specimen records with barcode numbers while barcoding.
Jan. 20, 2020

​Associating Barcode Numbers with Accession Numbers Video
​This video demonstrates how to perform the "Associating Barcode Numbers with Accession Numbers Protocol" (see above).
Feb. 23, 2019

Barcode Order Form
This document should be filled out to set up an account with Reliance Barcode Solutions for the first time.
Oct. 5, 2018

Barcode Recommendations​​
This document shows an example barcode with an explanation of its different parts and describes how to order barcodes from Reliance. Quotes from alternative sources are provided.
Sept. 21, 2018

Barcoding Protocol (Step 1)
This protocol explains how to barcode specimens independently of any other digitization steps.
June 19, 2019

Batch Adding Annotations in CCH2
This protocol describes how to add annotations to many specimen records at one time.
Dec. 16, 2020

Checklist Creation in CCH2
This guide describes how to create taxon checklists in CCH2 or a general Symbiota portal
Nov. 22, 2019

Combined Imaging + Barcoding Protocol (Step 1.2)
​This protocol describes how to image previously barcoded specimens using the Ortery lightbox setup and Smart Shooter 3.
Aug. 5, 2020

Data Cleaning with the Taxonomic Cleaning Tool (Video)
This video demonstrates how to use the taxonomic cleaning tool in the administration control panel to clean and standardize taxonomic names of your specimens.
Aug. 11, 2020

Full CAP Digitization Manual
This manual provides an overview of the project, goals, workflows, equipment recommendations and instructions, protocols, and a guide to using the portal, all wrapped into one document.
​NOTE: This manual is under construction.
Aug. 10, 2020

Georeferencing with GeoLocate (Batch Georeferencing) Protocol
This document describes how to batch georeference specimen records using the GeoLocate instance on the CCH2 portal.
Jan. 28, 2020

Imaging Overview Flowchart
This flowchart visualizes the imaging process, breaking it down into a number of smaller tasks.
Jan. 2, 2019

Image Processing Protocol
​(Step 3)

This protocol should be used by supervisors or trained technicians to process folders of raw images. Processing steps include adding metadata, cropping, adjusting highlights and lights, adjusting sharpening, and exporting raw images as DNG and JPEG files.
Aug. 5, 2020

Image Processing Software Recommendations
This document lists the recommended software for imaging and image processing.
Feb. 19, 2019

Imaging Protocol (Step 2)
This protocol describes how to image previously barcoded specimens using the Ortery lightbox setup and Smart Shooter 3.
Aug. 5, 2020

Imaging Protocol Video
​This video demonstrates how to image specimens using the Ortery lightbox setup and Smart Shooter 4.
Aug. 10, 2020

Imaging Station Equipment Recommendations
This document describes the recommend equipment and software to acquire for specimen imaging and image processing.
July 31, 2020

Instructions for Uploading Snapshot Data to CCH2
This document describes how to upload an entire collection dataset for institutions that have chosen to serve a “snapshot” of their collection database on CCH2 rather than managing it live.
Feb. 19, 2019

Introduction to CAP PowerPoint Presentation
This presentation is provided for CAP collaborators to use for introducing the CAP project in public and classroom settings. Users are encouraged to edit and augment the presentation however they see fit, so long as proper attribution of figures and images remain intact.
Oct. 10, 2019

Label Transcription Guide
​(Data Entry Protocol)
This protocol describes how to transcribe label  and annotation data from specimen images in the CCH2 portal.
Jan. 20, 2020

List of Taxa to be Digitized
This list contains the target taxa to be digitized as part of the CAP TCN grant. Note that many institutions may choose to digitize their entire collection, if feasible, rather than take the extra time to pull out specimens of the target taxa.
Nov. 7, 2019

Phenological Scoring Protocol
This protocol describes how to use the phenological scoring tools in CCH2. Taxon-specific protocols will soon be found on the Phenological Scoring Page.
Mar. 5, 2020

Poster, Year 2
This poster give an introduction to the network, the project, and our current progress toward our goals, as well as how researchers and members of the public can get involved. CAP Network members: feel free to edit as desired to highlight the work and progress at your herbarium.
Mar. 25, 2020

Publishing to GBIF
This document describes how to set up a collection in CCH2 to automatically publish their collection data to GBIF. This process need only be done once per institution.
Aug. 21, 2019

​Phenological Standards Article (APPS, Yost et al. 2018)
This article, titled "Digitization protocol for scoring reproductive phenology from herbarium specimens of seed plants," provides preliminary methods by which phenological data can be captured and stored in accordance with current metadata standards.
​Feb. 28, 2018

Symbiota Guide / Guide to Using the CCH2 Portal
This guide describes the many functions of the new Symbiota-based data portal, CCH2, and how to use many of these functions.
Oct. 23, 2019

Uploading Images to CyVerse and Loading into CCH2 (Step 4)
This protocol describes how a supervisor or trained technician can upload specimen images to CyVerse, which will then make these images web-accessible. The URLs for these images will then be linked to the specimen records in the CCH2 portal.
July 8, 2020

​Workflow Diagram
This diagram visualizes the overall digitization process as a series of steps. The steps are colored according to the type of person who is responsible for completing these steps. Note that the workflow demonstrates the steps to be completed for any given specimen, and these steps may be occurring simultaneously for different specimens.
June 19, 2019

Meeting Recordings

All-collaborator meeting, August 20, 2019

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This project made possible by National Science Foundation Award 1802312.
Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.


Poppy images courtesy of Matt Ritter

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