the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
Ordovician to Silurian graptolite specimen images for global correlation and shale gas exploration
Yan-Sen Chen
Xuan Ma
Xiao-Jing Tong
Yi-Tong Sun
Xiao-Yan Dong
Dan-Ni Fan
Shuang-Shuang Song
Yan-Yan Zhu
Ning Yang
Qing Xia
Abstract. Multi- elemental and -dimensional data are more and more important during the development of data-driven research, as is the case in modern palaeontology, in which visual examination, by experts or someday the artificial intelligence, to every fossil specimen acts a crucial and fundamental role. We here release an integrated image dataset of 113 Ordovician to Silurian graptolite species or subspecies that are significant in global stratigraphy and shale gas exploration. The dataset contains 1550 high-resolution graptolite specimen images and scientific information related to the specimen, e.g., every specimen's taxonomic, geologic, geographic, and related references. We develop a tool, FSIDvis (Fossil Specimen Image Dataset Visualiser), to facilitate the human-interactive exploration of the rich-attribution image dataset. A nonlinear dimension reduction technique, t-SNE (t-Distributed Stochastic Neighbor Embedding), is employed to project the images into the two-dimensional space to visualise and explore the similarities. Our dataset potentially contributes to the analysis of the global biostratigraphic correlations and improves the shale gas exploration efficiency by developing an image-based automated classification model. All images are available from https://doi.org/10.5281/zenodo.5205216 (Xu, 2021).
Hong-He Xu et al.
Status: final response (author comments only)
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CC1: 'Comment on essd-2021-280', Zhibin Niu, 14 Nov 2021
Our interactive visual explore of graptolite specimen image data (FSIDVIS) can be accessed through http://fsidvis.fossil-ontology.com:8089/ . Hit the spacebar to view the details of graptolite specimen. We also welcome comments and suggestions of the visual exploration tool.Â
Citation: https://doi.org/10.5194/essd-2021-280-CC1 -
AC1: 'Reply on CC1', Honghe Xu, 18 Nov 2021
Thank you for your comments.
The fossil specimen image dataset visualization (FSIDVIS) system is for everyone who needs detailed and scientific information of fossil specimens. We will add more data of fossil specimens to the system.
Citation: https://doi.org/10.5194/essd-2021-280-AC1
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AC1: 'Reply on CC1', Honghe Xu, 18 Nov 2021
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CC2: 'Comment on essd-2021-280', Zhaohui Pan, 14 Nov 2021
Graptolites are widely used as index fossils for determining rock ages and biostratigraphic correlations from the Middle Ordovician to the Telychian of the Silurian period. 1,550 high-resolution images of 41 genera and 16 families of Graptolites were never seen before. This is a high-quality dataset. Images with high quality in this dataset are well helpful for geological surveys and field practice in China. However, this is a dataset instead of a handbook. There are limits in the fieldwork. Why not develop an automated classification application or an e-book on a cellphone based on these graptolite data? Did you try the automatic classification?
In addition, there is a photo scale in Figure 3. But images in Figure 4 have no plotting scales. Do they have the same scale?Citation: https://doi.org/10.5194/essd-2021-280-CC2 -
AC2: 'Reply on CC2', Honghe Xu, 18 Nov 2021
Thank you for your comments.
Graptolites were originated in the Cambrian and extinct in the Devonian. As a kind of extinct organism, graptolites are significant for the role of dating sediments and macro-evolution research. In the study and the dataset we released, we only chose 113 species of graptolites from the mid Ordovician to early Silurian of China. these species of graptolite, though being a small amount of the whole group, are important to shale gas exploration and biozone recognizing. The specimens images of these species have their potential significances to shale gas exploration.
The uploaded dataset includes high-quality images, and every image shows clear and specific morphology of fossil organism and has its scientific name. We believe they can, to some extent, meet the demands of shale gas bed determination. We added scale bar to some specimens, but not illustrated them in the manuscript. That is why you see rules in the figure 3. We are also training the artificial intelligence (AI) model of automated classifying and identifying, the demonstration version is online (http://aifossil.fossil-ontology.com/#/). To the AI model, there is no need to show the scale bar.
The fossil specimen image dataset visualization (FSIDVIS) system is for everyone who needs detailed and scientific information of fossil specimens. But now the limitation is that we only uploaded and prepared data of 1550 graptolite speciemsn. Of course this is just a start. More specimens and the related e-book or searching system for mobile devices will follow. Â
Citation: https://doi.org/10.5194/essd-2021-280-AC2 -
CC3: 'Reply on AC2', Min Zhu, 19 Nov 2021
That sounds great. Please inform me when you publish the e-book or application on mobile devices.
Citation: https://doi.org/10.5194/essd-2021-280-CC3
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CC3: 'Reply on AC2', Min Zhu, 19 Nov 2021
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AC2: 'Reply on CC2', Honghe Xu, 18 Nov 2021
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CC4: 'Comment on essd-2021-280', Ting Nie, 19 Nov 2021
It’s thrill to see the work about the database guarantees multidimensional information of the fossil records. No doubt that the database empowered the research of palaeontology and the application in the shale gas exploration. More are supposed to come to publish in the future. Looking forward to the development of data-driven research in the field of palaeontology.
Citation: https://doi.org/10.5194/essd-2021-280-CC4 -
RC1: 'Comment on essd-2021-280', Anonymous Referee #1, 23 Nov 2021
The comment was uploaded in the form of a supplement: https://essd.copernicus.org/preprints/essd-2021-280/essd-2021-280-RC1-supplement.pdf
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AC3: 'Reply on RC1', Honghe Xu, 07 Dec 2021
Thank the reviewer’s comment and the detailed supplementary file. We specifically revised the manuscript and hopefully we will have it submitted soon.
We re-organized all images and assured that every specimen image shows with the scale in its own photo or separated photo. Now the updated dataset includes 2951 images and the whole size is 10.4 G. every scaled photo file is named with a postfix S. The image name consists of the number of specimen and the species name. one only troubleis that the volume of the whole dataset is quite large. It takes a while to upload and download all files.
The purposed of our study is not only providing an access of the gallery of graptolite specimens, but also showing that the image dataset is usable in data analysis and visualization and potentially using artificial intelligence.
The FSIDvis is an interactive visual explorer of graptolite specimen image data (FSIDvis), which is accessed through:
http://fsidvis.fossil-ontology.com:8089/
Hit the spacebar to view the details of graptolite specimen.
TSNE, or t-SNE (t-Distributed Stochastic Neighbor Embedding) is a technique for dimensionality reduction that is particularly well suited for the visualization of high-dimensional datasets that our specimens image dataset belongs to. We tried to analyze these data using this method and show a feasible way to classifying these specimens based on images only. Â
In the revised version we will invite a native English editor to proofread the whole manuscript. Thank you for your kind comment.
Some specimens were collected several years ago. Some of them were renamed and transferred. Species emendations were based on suggestions from experts of Nanjing Institute, we will give their named in the revision. We will make a further revision and state all the related issues. Â
Citation: https://doi.org/10.5194/essd-2021-280-AC3
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AC3: 'Reply on RC1', Honghe Xu, 07 Dec 2021
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RC2: 'Comment on essd-2021-280', Anonymous Referee #2, 04 Feb 2022
The comment was uploaded in the form of a supplement: https://essd.copernicus.org/preprints/essd-2021-280/essd-2021-280-RC2-supplement.pdf
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AC4: 'Reply on RC2', Honghe Xu, 25 Feb 2022
Thank the reviewer for the comment.
The main problem comprises two aspects, the dataset quality and the tool. We made the revision accordingly. Furthermore, the whole text is revised in text and writing by colleagues. Hoping this version is much better.
The dataset is updated and the newly uploaded to share. A new DOI is given in the revision.
https://doi.org/10.5281/zenodo.619494
Now it is ensured that every specimen is shown with additional scale bar and that any measurement to the fossil is available.
The reviewer also stated that some images are not quite clear, or some images seem too empty. These are all problem of image quality. The new dataset, with more hi-resolution images and scale, some microscope images were selected for the case that the fossil itself is small but the whole specimens is quite large. Â
The tool, FSIDvis, is updated and more detailed instruction of this software is given.
The naming system or the method is explained in the text. Every image file is named after its unique number and labeled species name. When the specimens wad re-studied or transferred to another taxon, the file name does not reflect its taxonomic status. a brief revision record is given in the updated tool, FSIDvis. And I also suggest that readers or users of our dataset check our spreadsheet file for detailed information.
Citation: https://doi.org/10.5194/essd-2021-280-AC4
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AC4: 'Reply on RC2', Honghe Xu, 25 Feb 2022
Hong-He Xu et al.
Data sets
High-resolution images of 1550 Ordovician to Silurian graptolite specimens for global correlation and shale gas exploration Xu, Honghe https://doi.org/10.5281/zenodo.5205216
Hong-He Xu et al.
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