What are raw scientific images? #1
Replies: 4 comments 5 replies
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Hi @ariannazuanazzi, A couple of thoughts:
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My definition of this means that if your hardware is producing digital outputs, raw and primary images are the same. |
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Raw scientific images are the original images taken by the imaging device with no modifications. They are unprocessed and displayed in their native appearance and initially created in a vendor’s proprietary file format that might include metadata to describe image acquisition conditions. They ought to be retained and then modifications should happen in generated copies. Also, some journals require the raw imaging data to be included in the supplementary. |
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Hi @ariannazuanazzi & thanks to @selgebali for pointing me this way. As background (2), I’m a member of the Open Microscopy Environment (OME) and helped to develop the Image Data Resource (IDR). We work with, e.g., multi-terabyte images from light and electron microscopy as well as from other domains. These images are regularly at least 5 dimensional (3D plus time and multiple channels of acquisition). We are currently working on a next-generation file format (NGFF) (see https://idr.github.io/ome-ngff-samples for example data) that we would love to also see hosted on Zenodo. Various talented folks including @oeway and @manzt have spent time looking into how to integrate our types of images into Zenodo and have filed various issues over the last few years. (1) Speaking for my users, the definition of raw scientific images (in terms of “please capture this data”) is that which is directly acquired by the microscopes. There still isn’t a sufficient level of trust in conversions to get rid of this data. (There are definitely exceptions like super resolution where the input images are less frequently used once the data has been processed, much more similar to NGS.) These original file formats, often proprietary and over 160 in number, are known to be poorly accessible remotely (e.g. from the web) and that is one of the main motivations for NGFF. For more background, see https://www.nature.com/articles/d41586-023-03064-9 |
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Hi!
As part of the Open Seeds program by OLS [https://openlifesci.org/openseeds/], we are building an open community repository for raw scientific images on Zenodo.
🧠 Scientific images are often not accessible to the general audience, educators, and visual artists whose work would benefit from images that portray real scientific spaces, methods, data, and discoveries.
💡 Part of the work that goes into the repository building is to define what raw scientific images are, according to people who work with scientific data in different disciplines. We would like your help!
📢 Please let us know
(1) what your definition of raw scientific images is - when you think of raw scientific images, what comes to mind?
(2) whether you work with scientific data and what your discipline/field/topic is (optional)
Thank you!
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