Authors Information

Authors name

Jonathan J. Ramtahal^{1, Kugako Sugimoto}1,3, Samantha Phan^{4, Tara Jambio Consortium*, Yumiko Patouillet}5, Romain Troublé^{6, Christine K. Luscombe}4, Sylvain Agostini^1,2

Affiliations

1. Shimoda Marine Research Center, University of Tsukuba, Shimoda 5-10-1, Shizuoka, 415-0025, Japan.
2. UMR-Entropie, IRD New Caledonia, Noumea, New Caledonia
3. Advanced Institute for Marine Ecosystem Change (WPI-AIMEC), Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan
4. pi-Conjugated Polymers Unit, Okinawa Institute of Science and Technology, Onna, Okinawa 904–0495, Japan.
5. Tara Ocean Japan, 2-25-2 Kamiosaki, Shinagawa, Tokyo, Japan
6. Fondation Tara Océan, Base Tara, 8 rue de Prague, 75012 Paris, France.

Contact

Jonathan J. Ramtahal (jonathan@shimoda.tsukuba.ac.jp / jonathanjramtahal@gmail.com )
Sylvain Agostini (agostini.sylvain@shimoda.tsukuba.ac.jp)

Introduction

This publication includes the dataset (image analysis) from the Tara-Jambio Joint Microplastic survey which consists of microplastic samples from locations across Japan in coastal areas (surface water and sediment).

List of files

• TaraJambio_Surface Water_ MP_Photos_Tours.zip: Photo dataset: each folder contains photos of the suspected microplastic particles per sample for surface water organized by sampling location.
  • Each location folder contains subfolders corresponding to individual sample. The subfolder are named according to Vial number, a unique identifier for each sample.
  • Each sample subfolder contains image files (.tiff), one text files of results from the image analysis (.txt), and an OjectJ file (.ojj) to reproduce the analysis. Obejct files (.ojj) which can be opened with the free software ImageJ (https://imagej.net/ij/) with the OjectJ plugin (https://sils.fnwi.uva.nl/bcb/objectj/index.html).
  • Location Names: Akkeshi, Amakusa, Asamushi, Hiroshima, Kadena Okinawa, Nagoya, Noto, Okayama, Onagawa, Onna Okinawa, Sado, Sesoko Nago, Shimane, Shimoda, Tateyama. See the zenodo dataset (doi:https://doi.org/10.5281/zenodo.14829995) for the exact GPS coordinates of each individual sample and location.
• TaraJambio_Sediment_MP_Photos_Tours.zip: Photo dataset: each folder contains photos of the suspected microplastic particles per sample for sediment organized by sampling location.
  • Each location folder contains subfolders corresponding to individual sample. The subfolder are named according to Vial number, a unique identifier for each sample.
  • Each sample subfolder contains image files (.tiff), one text files of results from the image analysis (.txt), and an ObjectJ file (.ojj) to reproduce the analysis. Object files (.ojj) which can be opened with the free software ImageJ (https://imagej.net/ij/) with the ObjectJ plugin (https://sils.fnwi.uva.nl/bcb/objectj/index.html).
  • Location Names: Akkeshi, Amakusa, Asamushi, Kadena Okinawa, Noto, Onagawa, Onna Okinawa, Sado, Sesoko Nago, Shimane, Shimoda, Takehara, Tateyama, Ushimoda. See the zenodo dataset (doi: https://doi.org/10.5281/zenodo.14829995) for the exact GPS coordinates of each individual sample and location.
• Column names for Resutls.txt files:
  • n: sequential number given to each object
  • rigid_particle_area: area of rigid type particles (mm2)
  • sheet_particle_area: area of sheet type particles (mm2)
  • fiber: length of fiber particles (mm)
  • feret_diam : feret diameter (mm)
  • picture_number: file name of photo

Additional computer code

Customs imagej macro were written to compute the surface areas of particles (individual and in batch).

• empty.ojj : object file used to initiate a new project. The files contains customs objects and results code.
• auto-analyze.ijm : Macro to 1. set a default particle type (rigid or sheet), 2. set the scale, 3. recognize individual particles based on threshold, 4. analyze particles using the "Anlyze function" from imagej, 5. create an objectj object for each individual particleand measure surface areas of particles, for each individual photos linked to the objectj project.
• change_type.ijm: Macro that allows to change the type (rigid, sheet) for each object from an objectj project.
• pitri-analysis-setup.ijm: Similar to "auto-analyze.ijm" but for batch analysis of multiple particles within one photo. This macro specifically detect particles on white background and adds the detected particles to the imagej roi. It should be run first when analyzing batch particle photos.
• count-plastics.ijm: After running "pitri-analysis-setup.ijm", this macro allows to go through each individual particles detected and to attribute a type (rigid, sheet or fibre).
• feret_diam.ijm: Macro to compute the feret diameter of rigid and sheets particle object for an entire objectj project.
• scale_batch_1.6x.ijm: Macro to attribute a scale of 275 pixel/mm to all photos linked to a objectj project.
• scale_batch_1mm.ijm: Macro to attribute a scale of 230 pixel/mm to all photos linked to a objectj project.
• scale_batch_5mm.ijm: Macro to attribute a scale of 80 pixel/mm to all photos linked to a objectj project.