Data from: Organic epidermal and cellular preservation in a 290-million-year-old amphibian unveils tetrapod skin evolution

This dataset compiles the images and data used in the preparation of the manuscript “Organic epidermal and cellular preservation in a 290-million-year-old amphibian unveils tetrapod skin evolution” by Antoine Logghe and co-authors. The dataset contains: the images used in the figure panels presented in the manuscript. File names start in Fig or SupplFig. the raw images and data, as well as pre-processed data used to generate the figure panels. File names start with the name of the method used to generate the data. Metadata are documented in the filenames, which include identifiers for the corresponding figure panel, the data type, whether the file contains raw or processed data, and—when applicable—the location of point analyses. Detailed descriptions of the methods used to collect and generate the data are provided in the manuscript. Usage notes for multispectral images (file names starting in multispectral_image): Unlike optical photographs, these images cannot be open and visualized as easily because they are 16-bit grayscale images and are low-intensity luminescence images collected with long exposure times; the luminescence signal can be so low that only the first hundreds of levels of grey out the 65,535 available are used, therefore making the image look all dark when opened using classical computer viewers (they read RGB or 8-bit encoding, not 16-bit). Consequently, these images are visualized and processed using viewers/software that allows for intensity adjustments of such 16-bit images. We recommend usage of the freeware ImageJ/FIJI, which is also used to generate false color RGB overlays by combining 3 of the raw images. In ImageJ/FIJI, individual .tif photoluminescence images (one by one or by selecting several at once) can be opened by simply dragging and dropping the file(s) into ImageJ/Fiji. Intensity adjustments can then be made by using the ">Image > Adjust > Brightness/contrast" tool, either automatically by using the “auto” button, or manually by setting minimum and maximum values using the slider thumbs or using the “set” button. False colour RGB overlays are also generated In ImageJ/FIJI. Following the above guidelines, this requires to open at least 3 individual .tif images. The images are then gathered into a stack using the ">Image > Stacks > Images to Stack" tool. (Note that intensity adjustment at this stage is based on the minimum and maximum values of all the opened images, so that some might appear all dark in the stack, this is normal and will be changed later). In some versions of ImageJ/FIJI, the number of images present in the stack is considered to be “Slices (z)” in the “>Image >Properties…” module, but it should be in “Channels (c)” for the generation of our RGB overlays, so these numbers need to be inverted. Note that image registration might be needed, and in this work it was acheived using ImageJ's Template Matching plugin. The RGB overlay can now be generated by using the “>Image >Color >Make Composite” tool (Display Mode “Composite”); the first image in the stack is now given a red (R) scale instead of a grey scale, the second is given a green (G) scale and the third a blue (B) scale (Note that up to 7 images (channels) can be assembled into such a “composite”; in that case the 4th image will be given a grey scale, the 5th image a cyan scale, the 6th a magenta scale and the 7th a yellow scale. Note also that generating images overlaying more than just 3 channels is possible but makes image interpretation much harder afterwards and is therefore not recommended). Once the “Composite” is created, the “> Brightness/contrast" tool can be used as described above to adjust the intensity of the different images (Note that intensity adjustments will affect the image/channel presently selected within the stack, such that adjustments need to be made for each image). The color scales can be changed using the “>Image >Color >Channels Tool…” tool, which allows for the display of all or some of the channels present in the stack and using the “More »” button to change the color scale used for the image/channel presently selected within the stack. the R scripts used to plot and/or process some of the data, and to generate some of the figure panels. File names start in R_script_. The R scripts are fully commented to document the data processing and plotting steps. To execute them, only a single line specifying the working directory (i.e., the location where the data are stored) needs to be modified, after which the remainder of the code can be run.