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Photo images, 3D models and CT scanned data of loaches (Botiidae, Cobitidae and Nemacheilidae) of Japan

Latest version published by Biodiversity Data Journal on Apr 29, 2018 Biodiversity Data Journal

Loach is one of the major cypriniform fishes in freshwater habitats of Japan, being recognized 23 described species/subspecies and 12 undescribed/undecides clades (Nakajima and Uchiyama 2017) (http://ffish.asia/loachesOfJapan). As well as molecular genetic research (Kitagawa et al. 2001a, Kitagawa et al. 2001b, Kitagawa et al. 2003a, Kitagawa et al. 2003b, Kitagawa et al. 2005, Suzawa 2006, Morishima et al. 2008, Saitoh et al. 2010, Kano et al. 2011, Miyazaki et al. 2011, Shimizu et al. 2011, Kano et al. 2012, Nakajima 2012, Nakajima 2016, Nakajima and Suzawa 2016, Nakajima and Uchiyama 2017), morphological examinations are needed for further development of loach study. Digital archiving of fish specimens is one of the progressive challenges in ichthyology for open science (Kanagawa Prefectural Museum of Natural History and National Museum of Nature and Science 1998, Berquist et al. 2012, Kano et al. 2013, Kano et al. 2016). This paper aimed to online publish photo images, 3D models and CT scanned data of all the known taxa/clades of loaches inhabiting in Japan (http://ffish.asia/loachesOfJapan3D) for the advances of loach study and ichthyology, and furthermore as a challenge of open science for public interests of biology.

Data Records

The data in this occurrence resource has been published as a Darwin Core Archive (DwC-A), which is a standardized format for sharing biodiversity data as a set of one or more data tables. The core data table contains 103 records.

This IPT archives the data and thus serves as the data repository. The data and resource metadata are available for download in the downloads section. The versions table lists other versions of the resource that have been made publicly available and allows tracking changes made to the resource over time.

Downloads

Download the latest version of this resource data as a Darwin Core Archive (DwC-A) or the resource metadata as EML or RTF:

Data as a DwC-A file download 103 records in English (9 KB) - Update frequency: irregular
Metadata as an EML file download in English (25 KB)
Metadata as an RTF file download in English (16 KB)

Versions

The table below shows only published versions of the resource that are publicly accessible.

How to cite

Researchers should cite this work as follows:

Kano Y (2018): Photo images, 3D models and CT scanned data of loaches (Botiidae, Cobitidae and Nemacheilidae) of Japan. v1.2. Biodiversity Data Journal. Dataset/Occurrence. http://ipt.pensoft.net/resource?r=jp_loaches_3dct_models&v=1.2

Rights

Researchers should respect the following rights statement:

The publisher and rights holder of this work is Biodiversity Data Journal. This work is licensed under a Creative Commons Attribution Non Commercial (CC-BY-NC) 4.0 License.

GBIF Registration

This resource has not been registered with GBIF

Keywords

3D model; Anatomy; Bone; CT scan; Digital archiving; Fish specimen; Freshwater fishes of Japan; GBIF; Holotype; Loach; Morphology; Open science; Paratype; Skeleton; Undescribed species; Inventorythematic

External data

The resource data is also available in other formats

loachesOfJapanhttp://ffish.asia/loachesOfJapan UTF-8 html; jpg
loachesOfJapan3Dhttp://ffish.asia/loachesOfJapan3D UTF-8 html; Wavefront object format (.obj); CT dicom file (.dcm)

Contacts

Who created the resource:

Yuichi Kano
Associate Professor
Kyushu University 744 Motooka, Nishi-ku 8190395 Fukuoka-shi Fukuoka JP
http://fish.asia

Who can answer questions about the resource:

Yuichi Kano
Associate Professor
Kyushu University 744 Motooka, Nishi-ku 8190395 Fukuoka-shi Fukuoka JP
http://fish.asia

Who filled in the metadata:

Yuichi Kano
Associate Professor
Kyushu University 744 Motooka, Nishi-ku 8190395 Fukuoka-shi Fukuoka JP
http://fish.asia

Who else was associated with the resource:

Author
Yuichi Kano
Associate Professor
Kyushu University 744 Motooka, Nishi-ku 8190395 Fukuoka-shi Fukuoka JP
http://fish.asia
Author
Jun Nakajima
Research Worker
Fukuoka Institute of Health and Environmental Sciences 39 Mukaizano 8180135 Dazaifu Fukuoka JP
Author
Takeshi Yamasaki
Laboratory Chief
Yamashina Institute for Ornithology, Japan 115 Konoyama 2701145 Abiko-shi Chiba JP
Author
Jyun-ichi Kitamura
Curator
Mie Prefectural Museum 3060 Isshinden-kōzubeta 5140061 Tsu-shi Mie JP
Author
Ryoichi Tabata
Curator
Lake Biwa Museum 1091 Oroshimocho 5250001 Kusatsu Shiga JP

Geographic Coverage

Inland water habitats of Japan.

Bounding Coordinates South West [23, 123], North East [46, 150]

Taxonomic Coverage

No Description available

Kingdom  Animalia (Animals)
Phylum  Chordata (Chordates)
Subphylum  Craniata (Vertebrat es and hagfishes)
Class  Osteichthyes (Bony fishes and tetrapods)
Order  Cypriniformes (Carps, loaches, minnows and relatives)
Family  Botiidae (Botiid loach),  Cobitidae (True loaches),  Nemacheilidae (Stone loaches)
Species  Parabotia curtus ("Ayumodoki"),  Cobitis kaibarai ("Ariake-suji-shima-dojyô"),  Cobitis magnostriata ("Oogata-suji-shima-dojyô"),  Cobitis matsubarae ("Yamato-shima-dojyô"),  Cobitis sp. "yamato" complex Type A ("Yamato-shima-dojyo" (Type A)),  Cobitis sakahoko ("Oyodo-shima-dojyô"),  Cobitis shikokuensis ("Hina-ishi-dojyô"),  Cobitis sp. BIWAE type A ("Oo-shima-dojyô"),  Cobitis sp. BIWAE type B ("Nishi-shima-dojyô"),  Cobitis sp. BIWAE type C ("Higashi-shima-dojyô"),  Cobitis sp. BIWAE type D ("Tosas-shima-dojyô"),  Cobitis takatsuensis ("Ishi-dojyô"),  Cobitis takenoi ("Tango-suji-shima-dojyô"),  Misgurnus anguillicaudatus (Clade B1) ("Dojyô" (Japan clade)),  Misgurnus anguillicaudatus (Clade B2) ("Dojyô" (China clade)),  Misgurnus anguillicaudatus (jindai) ("Jindai-dojyô"),  Misgurnus sp. (Clade A) ("Kita-dojyô"),  Misgurnus sp. IR ("Shinobi-dojyô"),  Misgurnus sp. OK ("Hyoumon-dojyô"),  Misgurnus dabryanus ("Kara-dojyô"),  Niwaella delicata ("Ajime-dojyô"),  Barbatula oreas ("Fuku-dojyô"),  Lefua costata ("Hime-dojyô"),  Lefua echigonia ("Hotoke-dojyô"),  Lefua nikkonis ("Ezo-hotoke-dojyô"),  Lefua sp. 1 ("Nagare-hotoke-dojyô"),  Lefua sp. 2 ("Tôkai-nagare-hotoke-dojyô")
Subspecies  Cobitis minamorii minamorii ("San'yô-kogata-suji-shima-dojyô"),  Cobitis minamorii oumiensis ("Biwa-kogata-suji-shima-dojyô"),  Cobitis minamorii saninensis ("San'in-kogata-suji-shima-dojyô"),  Cobitis minamorii tokaiensis ("Tôkai-kogata-suji-shima-dojyô"),  Cobitis minamorii yodoensis ("Tôkai-kogata-suji-shima-dojyô"),  Cobitis striata fuchigamii ("Onga-suji-shima-dojyô"),  Cobitis striata hakataensis ("Hakata-suji-shima-dojyô"),  Cobitis striata striata ("Chûgata-suji-shima-dojyô")

Temporal Coverage

Start Date / End Date 1954-06-06 / 2017-12-15

Project Data

No Description available

Title Developing a integrated database for biodiversity
Funding This work was partially supported by JSPS KAKENHI Grant Number 18HP8029.

The personnel involved in the project:

Sampling Methods

The specimens were generally captured by a hand-net in the fields.

Study Extent Specimens of loaches of Japan were collected from personal collections and museums.

Method step description:

  1. Photo images were taken in the fields by capturing individuals (Kano and Nakajima 2014) and/or by snorkeling. The formalin-fixed specimens were also photographed in the laboratory followed by CT scanning (Aloka Latheta LCT-200, Hitachi, Ltd.). 3D surface (CT value: -400 to -40) and skeletal (CT value: 5 to 200) models were extracted from the CT data. The CT data in raw file format was also stored and available on the web.

Collection Data

Collection Name JNC/JNCP (J. Nakajima's personal collection)
Collection Name KPM (Kanagawa Prefectural Museum of Natural History)
Collection Name LBM (Lake Biwa Museum)
Collection Name MPM/MPMQ (Mie Prefectural Museum)
Collection Name OMNH (Osaka Museum of Natural History)
Collection Name QUYK (Y. Kano's personal collection)
Collection Name TKPM (Tokushima Prefectural Museum)
Specimen preservation methods Formalin

Additional Metadata

Alternative Identifiers http://ipt.pensoft.net/resource?r=jp_loaches_3dct_models