InsectBrainDatabase - A unified platform to manage, share, and archive morphological and functional data
Preprint posted on 1 December 2020 https://www.biorxiv.org/content/10.1101/2020.11.30.397489v1
Article now published in eLife at http://dx.doi.org/10.7554/eLife.65376
Over the past fifty years, insect neuroscience has grown into a large field, partly because of genuine interest by researchers for specific species, such as the honeybee or the desert locusts, and partly because insect brains are much smaller than vertebrate brains. As the building blocks are the same, there is some hope to understand the principles of brain structure in insects and then be able to better understand the larger organs of our closer relatives and ourselves. Specifically, in the last ten years or so, advanced microscopy and single cell marking techniques have led to a fast advancement of the field. Immense amounts of anatomical and functional data have been collected by labs around the world, but most raw data have been barely accessible, making comparative studies and general advancement of the field more cumbersome than could be wished for. Several databases (including Virtual Fly Brain, FlyCircuit, FruitFlyObservatory) have been available for Drosophila. At the other end of the spectrum, the fast-growing site neuromorpho.org has collected (as of January 2021) over 3 million reconstructed neurons of almost 1000 types in 78 species including several species of insects, but is very vertebrate-based. A home for reconstructed neurons in a broader range of insect species has been lacking.
In their paper, the authors, an informal consortium of several European research groups, describe the InsectBrainDatabase (https://insectbraindb.org/app/ ), a free database that they have recently launched. So far, the database has 199 neurons from 17 species (see two glimpses in figure 1), but that seems just the start, and more importantly, each neuron is associated with its brain region, in a standardized 3D reconstruction of the brain in the study species. At each level, data from experiments can be linked and the database can be searched.
In their bioRxiv paper, the authors describe the database as well as its interactive search interfaces and potential uses. For instance, users can see and rotate a chosen neuron in a reconstructed brain of the species, changing transparency of the different regions as needed, but they can also compare the same neuron in up to four insect species at the same time, thus inviting to truly comparative work. While uploaded data are owned by the contributor and cannot be changed, they are publicly available and downloaded images can be used in publications under a Creative Commons Attribution 4.0 International (CC BY 4.0) licence, with credit to the original data owners and the IBdb.
The authors then go on and explain in much detail how new contributors can upload data on new species, new neurons and new experiments in the database. They seem to have a well- developed concept of curation and administration of data, so this may grow fast into something used by many.
Why I chose this paper
If read by many, this will be a very useful paper. Basically, it is a user guide for a new database, and having seen the volumes of data grow in the field of neurobiology, I have been wondering for a long time how science could make the most use of all the information. This paper and the described database will definitely do their share to help here, so I wish it as much publicity as possible, among insect neurobiologists, but also amongst all researchers interested in comparative brain research.
It goes without saying that the new database is a very useful new tool for all insect neurobiologist. My guess is that many people will add new data, and only then we will see its full potential. So check it out and add to it!
It may be equally important that the administrators keep contact with those colleagues that work on the other existing databases, such as http://neuromorpho.org/ and https://v2.virtualflybrain.org, to mention just two of them. This will be important to connect and make the most use of all of them, instead of competing, and will also help to keep up with future technology development.
Questions to the authors
- How long (months, years, decades) do you expect curators to provide their service – and what happens later?
- Will the remaining parts of the insect nervous system be added at some point?
- For the far future, is there a plan to expand towards pancrustaceans?
Posted on: 22 February 2021Read preprint
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