Hiromune Mitsuhashi

We would like to introduce our recently developed systems for taking images of herbarium specimens and for the automatic extraction of data from specimen labels at the Herbarium of the Museum of Nature and Human Activities, Hyogo, Japan (HYO). Firstly, we designed a low-cost, but high-quality specimen imaging system for non-professional photographers to obtain images rapidly (Takano et al. 2019). Our system uses a mass-produced, mirrorless single-lens reflex (SLR) camera (SONY ILCE6300) with a zoom lens (Samyang Optics SYIO35AF-E35 mm F/2.8). We made a photo stand by ourselves to reduce costs. In addition, we have adopted an LED (light-emitting diode) lighting system with high color rendering. This imaging system has been introduced, with some improvements or adjustments for available space, to various herbaria in Japan (e.g., University of Tokyo (TI), Kyoto University (KYO)), contributing to the digitization of herbarium specimens across Japan. Next, we developed a system to extract label information from specimen images. The specimen image was uploaded to Google OCR and data were extracted in the form of text. Uploading the whole specimen image decreased the reading accuracy of the software because the plant images behaved as OCR (Optical Character Reader) noise. Therefore, the label part was cut out from the whole specimen image by using D-Lib*1 and uploaded to tesseract OCR*2 for OCR extraction of the label information (Aoki 2019, Takano et al. 2020). When installing this system for HYO, we designed it as an application accessible externally via the internet, which proved very useful during the coronavirus pandemic: part-time workers checked and conducted label data input from home. Finally, we decided to develop a system that would automatically label the text data extracted by OCR and input them into the appropriate cells of the database. Even though the text data could be extracted from specimen images, it needed a human to input them into the database. Therefore, we adopted Named Entity Recognition (NER), a system that extracts named entities such as place names, identifying proper nouns from unstructured text data. It enables information recorded in herbarium specimens to be tagged as named entities. We tried text matching at first, but the result was not satisfactory, so we started to use machine learning instead. We compared three natural language libraries for Japanese: BERT (Bidirectional Encoder Representations from Transformers), Albert (A Lite version of BERT), and SpaCy. Despite BERT and SpaCy returning similarly high f-scores (indicating good performance), we decided to use SpaCy because it runs better on ordinary PCs or servers. With sufficient machine learning after the creation of a text corpus (a specialised dataset) specific to labels on herbarium specimens, we successfully developed the application. The project files are available on GitHub*3 (Takano et al. 2024). We then examined whether this system could be applied to non-plant specimen images, i.e., fishes or birds, and found that it could efficiently extract data. Therefore, we decided to publicize this system on the cloud server and share it with other natural history museums in Japan*4. Curators can obtain a unique ID and password and upload specimen images from their collection to extract label data. The digitization of natural history collections in Japan has been long behind other countries, and this system will help to accelerate it. The system mentioned above is specialized for the natural history collections of Japan, but we believe it is possible to build similar programs in other countries, and we hope our experience will contribute to the mobilization of the world’s natural history collections.

Aim Natural disaster risk reduction (DRR) is becoming a more important function of protected area (PAs) for current and future global warming. However, biodiversity conservation and DRR have been handled separately and their interrelationship has not been explicitly addressed. This is mainly because, due of prevailing strategies and criteria for PA placement, a large proportion of PAs are currently located far from human-occupied areas, and habitats in human-occupied areas have been largely ignored as potential sites for conservation despite their high biodiversity. If intensely developed lowland areas with high flooding risk overlap with important sites for biodiversity conservation, it would be reasonable to try to harmonize biodiversity conservation and human development in human-inhabited lowland areas. Here, we examined whether extant PAs can conserve macroinvertebrate and freshwater fish biodiversity and whether human-inhabited lowland flood risk management sites might be suitable to designate as freshwater protected areas (FPAs). Location Across Japan. Methods We examined whether extant PAs can conserve macroinvertebrate and freshwater fish biodiversity and analysed the relationship between candidate sites for new FPAs and flood disaster risk and land use intensity at a national scale across Japan based on distribution data for 131 freshwater fish species and 1395 macroinvertebrate species. Results We found that extant PAs overlapped with approximately 30% of conservation-priority grid cells (1 km(2)) for both taxa. Particularly for red-listed species, only one species of freshwater fish and three species of macroinvertebrate achieved the representation target within extant PAs. Moreover, more than 40% of candidate conservation-priority grid cells were located in flood risk and human-occupied areas for both taxa. Main conclusions Floodplain conservation provides suitable habitat for many freshwater organisms and helps control floodwaters, so establishing new FPAs in areas with high flood risk could be a win-win strategy for conserving freshwater biodiversity and enhancing ecosystem-based DRR (eco-DRR).