How to Prepare Neuroanatomical Image Data (an Update)
Corresponding Author
Nathan J. O'Connor
MBF Bioscience, Williston, Vermont
Corresponding authors: [email protected]; [email protected]
Contribution: Conceptualization, Data curation, Methodology, Software, Supervision, Writing - original draft, Writing - review & editing
Search for more papers by this authorPaul J. Angstman
MBF Bioscience, Williston, Vermont
Contribution: Conceptualization, Supervision, Writing - review & editing
Search for more papers by this authorJeffrey O. Blaisdell
MBF Bioscience, Williston, Vermont
Contribution: Conceptualization, Data curation, Investigation, Methodology, Software, Supervision
Search for more papers by this authorChristopher D. Farnsworth
MBF Bioscience, Williston, Vermont
Contribution: Conceptualization, Investigation, Methodology, Software
Search for more papers by this authorCharles S. Gerfen
MBF Bioscience, Williston, Vermont
Contribution: Methodology, Software, Conceptualization, Supervision, Writing - review & editing
Search for more papers by this authorCorresponding Author
Jacob R. Glaser
MBF Bioscience, Williston, Vermont
Corresponding authors: [email protected]; [email protected]
Search for more papers by this authorCorresponding Author
Nathan J. O'Connor
MBF Bioscience, Williston, Vermont
Corresponding authors: [email protected]; [email protected]
Contribution: Conceptualization, Data curation, Methodology, Software, Supervision, Writing - original draft, Writing - review & editing
Search for more papers by this authorPaul J. Angstman
MBF Bioscience, Williston, Vermont
Contribution: Conceptualization, Supervision, Writing - review & editing
Search for more papers by this authorJeffrey O. Blaisdell
MBF Bioscience, Williston, Vermont
Contribution: Conceptualization, Data curation, Investigation, Methodology, Software, Supervision
Search for more papers by this authorChristopher D. Farnsworth
MBF Bioscience, Williston, Vermont
Contribution: Conceptualization, Investigation, Methodology, Software
Search for more papers by this authorCharles S. Gerfen
MBF Bioscience, Williston, Vermont
Contribution: Methodology, Software, Conceptualization, Supervision, Writing - review & editing
Search for more papers by this authorCorresponding Author
Jacob R. Glaser
MBF Bioscience, Williston, Vermont
Corresponding authors: [email protected]; [email protected]
Search for more papers by this authorPublished in the Neuroscience section
Abstract
Image data from a single animal in neuroscientific experiments can be comprised of terabytes of information. Full studies can thus be challenging to analyze, store, view, and manage. What follows is an updated guide for preparing and sharing big neuroanatomical image data. © 2024 Wiley Periodicals LLC.
Basic Protocol 1: Naming and organizing images and metadata
Basic Protocol 2: Preparing and annotating images for presentations and figures
Basic Protocol 3: Assessing the internet environment and optimizing images
Open Research
Data Availability Statement
All data presented in this manuscript are publicly available.
Literature Cited
- Burt, P. J. (1984). The pyramid as a structure for efficient computation. In A. Rosenfeld (Ed.), Multiresolution image processing and analysis (Vol. 12, pp. 6–35). Springer Series in Information Sciences, Springer. https://doi.org/10.1007/978-3-642-51590-3_2
- Dougherty, M. T., Folk, M. J., Zadok, E., Bernstein, H. J., Bernstein, F. C., Eliceiri, K. W., Benger, W., & Best, C. (2009). Unifying biological image formats with HDF5. Communications of the Association for Computing Machinery, 52(10), 42–47. https://doi.org/10.1145/1562764.1562781
10.1145/1562764.1562781 Google Scholar
- Edlow, B. L., Mareyam, A., Horn, A., Polimeni, J. R., Witzel, T., Tisdall, M. D., Augustinack, J. C., Stockmann, J. P., Diamond, B. R., Stevens, A., Tirrell, L. S., Folkerth, R. D., Wald, L. L., Fischl, B., & van der Kouwe, A. (2019). 7 Tesla MRI of the ex vivo human brain at 100-micron resolution. Scientific Data, 6, 244. https://doi.org/10.1038/s41597-019-0254-8
- Gaillard, F., Karten, H. J., & Sauvé, Y. (2013). Retinorecipient areas in the diurnal murine rodent Arvicanthis niloticus: A disproportionally large superior colliculus. Journal of Comparative Neurology, 521, 1699–1726. https://doi.org/10.1002/cne.23303
- Gerfen, C. R., Paletzki, R., & Heintz, N. (2013). GENSAT BAC Cre-recombinase driver lines to study the functional organization of cerebral cortical and basal ganglia circuits. Neuron, 80, 1368–1383. https://doi.org/10.1016/j.neuron.2013.10.016
- Kalinski, T., Zwönitzer, R., Grabellus, F., Sheu, S.-Y., Sel, S., Hofmann, H., & Roessner, A. (2011). Lossless compression of JPEG2000 whole slide images is not required for diagnostic virtual microscopy. American Journal of Clinical Pathology, 136, 889–895. https://doi.org/10.1309/AJCPYI1Z3TGGAIEP
- Karten, H. J., Glaser, J. R., & Hof, P. R. (2013). An important landmark in scientific publishing. Journal of Comparative Neurology, 521, 1697–1698. https://doi.org/10.1002/cne.23329
- Kyoda, K., Ho, K. H. L., Tohsato, Y., Itoga, H., & Onami, S. (2020). BD5: An open HDF5-based data format to represent quantitative biological dynamics data. PLoS One, 15(8), e0237468. https://doi.org/10.1371/journal.pone.0237468
- Mikula, S., Trotts, I., Stone, J. M., & Jones, E. G. (2007). Internet-enabled high-resolution brain mapping and virtual microscopy. NeuroImage, 35, 9–15. https://doi.org/10.1016/j.neuroimage.2006.11.053
- Moore, J., Basurto-Lozada, D., Besson, S., Bogovic, J., Bragantini, J., Brown, E. M., Burel, J. M., Moreno, X. C., de Medeiros, G., Diel, E. E., Gault, D., Ghosh, S. S., Gold, I., Halchenko, Y. O., Hartley, M., Horsfall, D., Keller, M. S., Kittisopikul, M., Kovacs, G., … Swedlow, J. R. (2023). OME-Zarr: A cloud-optimized bioimaging file format with international community support. Histochem Cell Biology, 160, 223–251. https://doi.org/10.1007/s00418-023-02209-1
- O'Connor, N. J., Tappan, S., & Glaser, J. (2014). How to prepare neuroanatomical image data. Current Protocols in Neuroscience, 69, 1.21.1–1.21.14. https://doi.org/10.1002/0471142301.ns0121s69
- Rossner, M., & Yamada, K. M. (2004). What's in a picture? The temptation of image manipulation. Journal of Cell Biology, 166, 11–15. https://doi.org/10.1083/jcb.200406019
- Sullivan, A. E., Tappan, S. J., Angstman, P. J., Rodriguez, A., Thomas, G. C., Hoppes, D. M., Abdul-Karim, M. A., Heal, M. L., & Glaser, J. R. (2022). A comprehensive, FAIR file format for neuroanatomical structure modeling. Neuroinform, 20, 221–240. https://doi.org/10.1007/s12021-021-09530-x
- Tuominen, V. J., & Isola, J. (2009). The application of JPEG2000 in virtual microscopy. Journal of Digital Imaging, 22, 250–258. https://doi.org/10.1007/s10278-007-9090-z
- Ueda, H. R., Ertürk, A., Chung, K., Gradinaru, V., Chedotal, A., Tomancak, P., & Keller, P. J. (2020). Tissue clearing and its applications in neuroscience. Nature Reviews Neuroscience, 21, 61–79. https://doi.org/10.1038/s41583-019-0250-1
- Weinstein, R. S., Graham, A. R., Richter, L. C., Barker, G. P., Krupinski, E. A., Lopez, A. M., Erps, K. A., Bhattacharyya, A. K., Yagi, Y., & Gilbertson, J. R. (2009). Overview of telepathology, virtual microscopy, and whole slide imaging: Prospects for the future. Human Pathology, 40, 1057–1069. https://doi.org/10.1016/j.humpath.2009.04.006
- Wilkinson, M. D., Dumontier, M., Aalbersberg, I. J., Appleton, G., Axton, M., Baak, A., Blomberg, N., Boiten, J. W., da Silva Santos, L. B., Bourne, P. E., Bouwman, J., Brookes, A. J., Clark, T., Crosas, M., Dillo, I., Dumon, O., Edmunds, S., Evelo, C. T., Finkers, R., … Zhao, J. (2016). FAIR Guiding Principles for scientific data management and stewardship. Scientific Data, 3, 160018. https://doi.org/10.1038/sdata.2016.18
