How to… image availability
I said this before, but it should be said again: Make a copy of your original microscope/image file before starting any processing and adjustments and then store this image file along with the final, processed image somewhere save. In an ideal world your colleagues should see your final published image figure and be able to re-do the analysis to get there from a provided microscope image. Ideally, nobody would need to ask you, i.e., the files (TIFFimage, PNG image, scripts, method, anaylsis pipeline etc) should be in a public repository. At present, finding authors and working email adresses is a lot of detective work with changing affiliation, Email, or even profession. This was “wonderfully” demonstrated recently. Researchers investigated how well “data available upon request” really works. To no ones surprise and in almost 50%, this did not even got an Email replies. The team then made “rigorous attempts to contact the authors”, i.e. continuously bothered the authors, which increased the data availability a little, but not enough (Tedersoo et al., 2021).
Public places for your data
For regular light microscope image techniques many public storage possibilities exist and should be used. Free options for up to 20-50Gb of image data are Zenodo, Open Science Framework, and Figshare. These repositories are broad and allow upload of any kind of digital data. A dedicated option for image data are OMERO servers, however these are usually maintained by institutions, rarely by individual labs and can be both public or private. Image data repositories, that are fully searchable are still being build. The BioImage Archive is one such attempt that accepts any image data, the Image Data Resource publishes image datasets that serves as reference datasets, and EMPIAR is a resource specifically for Electron Microscopy data.
Which files should be deposited?
The specific file type of the microscope image will depend on imaging setup. A standard format for loss-loss compression is TIFF or the open format OME-TIFF. In specialized microscopy techniques that rapidly accumulate tera-bites of data, e.g., long-term live-imaging, light-sheet microscopy, or similar the original microscopy files are often not stored locally and too large for public repositories. When only compressed files can be kept, PNG files are preferred to e.g., JPEG files, as they allow loss-less compression.
Read more:
The BioImage Archive - Building a Home for Life-Sciences Microscopy Data. 434, 167505. Hartley et al 2022 J Mol Biol.
A call for public archives for biological image data. Ellenberg et al 2018. Nat Methods.