An explanation of the provided open data files for the manuscript "Correlative Light, Electron Microscopy and Raman Spectroscopy Workflow to Detect and Observe Microplastic Interactions with Whole Jellyfish" 

Jessica Caldwell 1*, Céline Loussert-Fonta 1, Gaëlle Toullec 2, Niclas Heidelberg Lyndby 2, Beat Haenni 3, Patricia Taladriz-Blanco 4, Begońa Espińa 4, Barbara Rothen-Rutishauser 1, Alke Petri-Fink 1,5,*

1 Adolphe Merkle Institute, University of Fribourg, Chemin des Verdiers 4, 1700 Fribourg, Switzerland
2 Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Rte Cantonale, CH-1015 Lausanne, Switzerland
3 Institute of Anatomy, University of Bern, Baltzerstrasse 2, 3012 Bern, Switzerland
4 Water Quality Group, International Iberian Nanotechnology Laboratory (INL), Av. Mestre Jose Veiga s/n, 4715-330, Braga, Portugal
5 Department of Chemistry, University of Fribourg, Chemin du Musée 9, 1700 Fribourg, Switzerland

*Jessica Caldwell: jessica.caldwell@unifr.ch / jessic203@yahoo.com; Alke Petri-Fink: alke.fink@unifr.ch


The following repository contains .zip folders which are organized according to the figure they correspond to within the main manuscript and SI files.

The contents of each folder are as follow:

1. Folder Name: Figure2cLSMPreEmbed
	- A subfolder labelled "final" containing the final, processed images presented within the manuscript. The images are labelled with the type of microplastic particle they were exposed to in accordance with the labelling system presented in the manuscript.
	- A subfolder labelled "raw" containing the unprocessed LSM files. These files can be opened using the free software ImageJ or Fiji. Through this software color channels were separated, brightness and contrast adjustments were made, lookup tables were applied, and channels were merged to create one final composite that could be Z-projected and given a scale bar.

2. Folder Name: Figure3cLSMPostEmbed
	- A subfolder labelled "final" containing the final, processed images presented within the manuscript. The images are labelled with the type of microplastic particle they were exposed to in accordance with the labelling system presented in the manuscript. Furthermore, labels contain information about the processing steps used to obtain the final images.
	- A subfolder labelled "raw" containing the unprocessed LSM files. These files can be opened using the free software ImageJ or Fiji. Through this software color channels were separated, brightness and contrast adjustments were made, lookup tables were applied, and channels were merged to create one final composite that could be given a scale bar.

3. Folder Name: Figure4TEM
	- A subfolder labelled "final" containing the final, processed images presented within the manuscript. The images are labelled with the type of microplastic particle they were exposed to in accordance with the labelling system presented in the manuscript. Furthermore, labels contain information about the processing steps used to obtain the final images.
	- A subfolder labelled "raw" containing the unprocessed TEM and LSM files. All files can be opened using the free software ImageJ or Fiji. Through this software, for cLSM images the color channels were separated, brightness and contrast adjustments were made, lookup tables were applied, and channels were merged to create one final composite that could be given a scale bar. 
	  TEM images were gaussian blurred, brightness and contrast adjustments were made, the auto-generated black bar at the bottom of images was removed, a scale bar was added, and images were rotated to align with corresponding cLSM images.

4. Folder Name: Figure5Raman
	- All region of interest brightfield images and text files of spectral data were extracted from WITec proprietary Control 5 software. These files are labelled with the type of microplastic particle they were exposed to in accordance with the labelling system presented in the manuscript as well as all experimental conditions (e.g. gratings, scan integration times, accumulation numbers, objective magnification, and cosmic ray removal information).

5. Folder Name: FigureS1SEM
	- A subfolder labelled "final" containing the final, processed images presented within the manuscript. The images are labelled with the type of microplastic particle they were exposed to in accordance with the labelling system presented in the manuscript.
	- A subfolder labelled "raw" containing the unprocessed SEM files. All files can be opened using the free software ImageJ or Fiji. Through this software, SEM images were brightness and contrast adjusted, the auto-generated metadata bar at the bottom of images was removed, and a scale bar was added.
	- A .txt file containing the numerical sizing data collected and used to create the sizing box plot in Origin.

6. Folder Name: FigureS2SEMControl
	- A subfolder labelled "final" containing the final, processed images presented within the manuscript. The images are labelled with the indication that they were blanks and their corresponding scale bar size.
	- A subfolder labelled "raw" containing the unprocessed SEM files. All files can be opened using the free software ImageJ or Fiji. Through this software, SEM images were brightness and contrast adjusted, the auto-generated metadata bar at the bottom of images was removed, and a scale bar was added.

7. Folder Name: FigureS3EmbedAndSectionTest
	- A subfolder labelled "final" containing the final, processed images presented within the manuscript. The images are labelled with the type of microplastic particle they were exposed to in accordance with the labelling system presented in the manuscript and according to the thickness of the section that was imaged.
	- A subfolder labelled "raw" containing the unprocessed LSM files. These files can be opened using the free software ImageJ or Fiji. Through this software color channels were separated, brightness and contrast adjustments were made, lookup tables were applied, and channels were merged to create one final composite that could be given a scale bar.

8. Folder Name: FigureS4PETC1RG11Sequence
	- A subfolder labelled "final" containing the final, processed images presented within the manuscript. The images are labelled with the type of microplastic particle they were exposed to in accordance with the labelling system presented in the manuscript and according to the number the section was assigned (ascending chronologically so that section 1 was the first made and all subsequent sections were further inside the sample).
	- A subfolder labelled "raw" containing the unprocessed LSM files. These files can be opened using the free software ImageJ or Fiji. Through this software color channels were separated, brightness and contrast adjustments were made, lookup tables were applied, and channels were merged to create one final composite that could be given a scale bar. In some cases, rotation was also applied to make the orientation of the final images easier to comprehend.

9. Folder Name: FigureS5PET1Sequence
	- A subfolder labelled "final" containing the final, processed images presented within the manuscript. The images are labelled with the type of microplastic particle they were exposed to in accordance with the labelling system presented in the manuscript and according to the number the section was assigned (ascending chronologically so that section 1 was the first made and all subsequent sections were further inside the sample).
	- A subfolder labelled "raw" containing the unprocessed LSM files. These files can be opened using the free software ImageJ or Fiji. Through this software color channels were separated, brightness and contrast adjustments were made, lookup tables were applied, and channels were merged to create one final composite that could be given a scale bar. In some cases, rotation was also applied to make the orientation of the final images easier to comprehend.

10. Folder Name: FigureS6PPC1RG9Sequence
	- A subfolder labelled "final" containing the final, processed images presented within the manuscript. The images are labelled with the type of microplastic particle they were exposed to in accordance with the labelling system presented in the manuscript and according to the number the section was assigned (ascending chronologically so that section 1 was the first made and all subsequent sections were further inside the sample).
	- A subfolder labelled "raw" containing the unprocessed LSM files. These files can be opened using the free software ImageJ or Fiji. Through this software color channels were separated, brightness and contrast adjustments were made, lookup tables were applied, and channels were merged to create one final composite that could be given a scale bar. In some cases, rotation was also applied to make the orientation of the final images easier to comprehend.

11. Folder Name: FigureS7PP6Sequence
	- A subfolder labelled "final" containing the final, processed images presented within the manuscript. The images are labelled with the type of microplastic particle they were exposed to in accordance with the labelling system presented in the manuscript and according to the number the section was assigned (ascending chronologically so that section 1 was the first made and all subsequent sections were further inside the sample).
	- A subfolder labelled "raw" containing the unprocessed LSM files. These files can be opened using the free software ImageJ or Fiji. Through this software color channels were separated, brightness and contrast adjustments were made, lookup tables were applied, and channels were merged to create one final composite that could be given a scale bar. In some cases, rotation was also applied to make the orientation of the final images easier to comprehend.

12. Folder Name: FigureS8B4Sequence
	- A subfolder labelled "final" containing the final, processed images presented within the manuscript. The images are labelled with blank in accordance with the labelling system presented in the manuscript and according to the number the section was assigned (ascending chronologically so that section 1 was the first made and all subsequent sections were further inside the sample).
	- A subfolder labelled "raw" containing the unprocessed LSM files. These files can be opened using the free software ImageJ or Fiji. Through this software color channels were separated, brightness and contrast adjustments were made, lookup tables were applied, and channels were merged to create one final composite that could be given a scale bar. In some cases, rotation was also applied to make the orientation of the final images easier to comprehend.

13. Folder Name: FigureS9Grids
	- A subfolder labelled "final" containing the final, processed images presented within the manuscript. The images are labelled with d with the type of microplastic particle they were exposed to in accordance with the labelling system presented in the manuscript.
	- A subfolder labelled "raw" containing the unprocessed LSM files. These files can be opened using the free software ImageJ or Fiji. Through this software color channels were separated, brightness and contrast adjustments were made, lookup tables were applied, and channels were merged to create one final composite that could be given a scale bar. In some cases, rotation was also applied to make the orientation of the final images easier to comprehend.

14. Folder Name: FigureS10NoParticleTEM
	- A subfolder labelled "final" containing the final, processed images presented within the manuscript. The images are labelled with the type of microplastic particle they were exposed to in accordance with the labelling system presented in the manuscript. Furthermore, labels contain information about the processing steps used to obtain the final images.
	- A subfolder labelled "raw" containing the unprocessed TEM and LSM files. All files can be opened using the free software ImageJ or Fiji. Through this software, for cLSM images the color channels were separated, brightness and contrast adjustments were made, lookup tables were applied, and channels were merged to create one final composite that could be given a scale bar. 
	  TEM images were gaussian blurred, brightness and contrast adjustments were made, the auto-generated black bar at the bottom of images was removed, a scale bar was added, and images were rotated to align with corresponding cLSM images.

15. Folder Name: TableS1CharacterizationOfMPs
	- Text files containing all SEM sizing data obtained from multiple SEM images. The files are labelled with the type of microplastic particle in accordance with the labelling system presented in the manuscript. The top is a compiled list of lengths while the bottom contains all relevant parameters obtained from Fiji. These data were used to calculate minimum, average, and maximum diameters as well as their standard deviations.