Digitization workflows for flat sheets and packets of plants, algae, and fungi.Applications in plant sciences

A herbarium is a collection of preserved plant specimens and associated data used for scientific study. The oldest traditions of making herbarium collection can be traced back to Italy. Luca Ghini, who is an Italian physicians and botanists created herbaria with his students. The oldest extant plant specimen is GheradoCibo from around 1532 in the herbaria created by Luca (Bellorini, 2016). Nowadays, with the development of modern technologies such as DNA sequencing, digitization, and fine-scale geography, these advanced technologies are employed into the research and management of many contemporary herbariums to for accuracy purposes(Meineke, 2018). This paper will use the Wisconsin State Herbarium (WIS) as an example to highlight several technologies that have been used in current herbariums, and then explore the impacts of these technologies on the herbariums and finally discuss limitations and concerns of these technologies.

According to Mr. Mark Allen Wetter, the senior academic curator of WIS, almost every specimen (native and introduced) has provided two sequenced genes for a project named “Dimension of Biodiversity (DOB)”. The goal of this project is to better understand the evolutionary and genetic bases for plant diversity by integrating contemporary understanding of genetic, phylogenetic and functional diversity in temperate plants. Currently, researchers participating in this project are sequencing 2-3 identifier genes for most of the vascular plant specimens in Wisconsin to generate a robust phylogeny, thus inferring patterns of trait evolution and diversification as well as phylogenetic patterns in community assembly (Erickson et al, 2014). The researchers will then use the data generated by the DNA barcoding subproject to examine the association of ecological traits with phylogenetic tree, so that people can have deeper understanding of important ecological topics such as recent habitat fragmentation, colonization/extinction and geographic range.

However, it is very time consuming and costly to extract DNA from plants for sequencing. According to Foundation Plant Services (2018), it will cost $345 and three to four weeks to identify an unknown specimen. Therefore, the WIS does not use DNA sequencing to identify unknown specimen. Instead, faculty at the WIS uses the traditional method that has been used in the last few centuries: keying the specimens with floras and monographs, and then comparing the unknown to other verified specimens in the collection. However, one of the problems of this method is that if the specimen is sterile or relatively young, it is always impossible to identify the specimen successfully (Pace et al., 2018). Another problem of this technique is that the accuracy of the result of identification, sometimes, depends more on the level of expertise and flora knowledge of the person who identifies the plants. That is, the more exposure to the flora, the higher the chance a person can identify a specimen correctly.

Apart from using biotechnology to conduct research study, the WIS also use advanced electronic technology to digitize the specimens in the herbarium. It is noteworthy to point out that the WIS contributes specimen records to the repository of Integrated Digitized Biocollections (iDigBio) of the USA’s National Resources for Advancing Digitization of Biodiversity Collections (ADBC) funded by the National Science Foundation (Nelson et al., 2015). Through ADBC, data and images for millions of biological specimens are available in electronic format for the research community, government agencies, students, educators and the general public.

First, to digitize a specimen, volunteers and faculties at WIS attach a unique bar code to it. No two specimens anywhere in the world will have the exact same barcode, which minimizes confusion and makes retrieval of these specimens much easier than what was experienced in the past (WIS, 2018). After that, volunteers and faculties at WIS will record all of the information related to the specimens into the database. This information includes who collected the specimens, how many specimens have been assigned to this collection, where and when it was collected, as well as a brief description of the plant, habitat, GPS coordinates, other plants growing in the vicinity, etc.

The next step of digitization is the imaging of specimens. The photographers will use SLR camera to take pictures of the specimens. Before the shooting, a color card is putbelow the specimen. This is because the color card can be used to a calibrate computer monitor or adjust color if the specimen image is printed. Additionally, a herbarium stamp is also sealed on the specimen before imaging. Here, the WIS makes use of university’s mascot Bucky Badger. If this specimen is ever lent to other organizations, it is more likely to be returned to WIS because the stamp identifies it by origin.After imaging the specimen, the photographers will scan the bar code on the specimen and rename the filename so that the file name corresponds to the bar code. The photographers will also seal another stamp on the specimen to indicate that this specimen has been imaged. The final step of digitization is organizing specimens into different cabinets according to their phylogeny.

Although the process of digitization at WIS is not a smooth one, it is relatively smooth and continuous. WIS faces a number of challenges in the day-to-day basis of collection in other natural history collection of specimen.The digitization does not meet the accepted standards. The organization faces similar challenges other herbarium across the globe face in their operations (Vollmar et al., 2010). For instance, the imaging technique available in the herbarium is good, but it is not perfect. Adopting the new imaging could help taking perfect shots that will provide better photos of specimens to make learning easier and efficient. On the same note, another challenge that WIS is having is lack of automated systems of recording data especially during collection. Developed herbariums have working automated systems that do require there staff to apply anything manual in the whole process of specimen collection. Even though, there are some process that might require manual input of data, it better if the firm had more improvised ways data entry. Many at times, unnoticeable mistakes are likely to occur affecting the credibility of the recorded data. Many at times, this uneven digitization landscape can have a negative variation of data hence compromising it in the end and rendering unfit for use (Vollmar et al., 2010).