Notes
Shih, A. Y., Driscoll, J. D., Drew, P. J., Nishimura, N., Schaffer, C. B., & Kleinfeld, D. (2012). Two-photon microscopy as a tool to study blood flow and neurovascular coupling in the rodent brain. Journal of Cerebral Blood Flow and Metabolism, 32(7), 1277–1309, https://doi.org/10.1038/jcbfm.2011.196.
Lin, M. Z., & Schnitzer, M. J. (2016). Genetically encoded indicators of neuronal activity. Nature Neuroscience, 19(9), 1142–1153, https://doi.org/10.1038/nn.4359.
Drew, P. J., Blinder, P., Cauwenberghs, G., Shih, A. Y., & Kleinfeld, D. (2010). Rapid determination of particle velocity from space-time images using the Radon transform. Journal of Computational Neuroscience, 29(1–2), 5–11. https://doi.org/10.1007/s10827-009-0159-1.
Kim, T. N., Goodwill, P. W., Chen, Y., Conolly, S. M., Schaffer, C. B., Liepmann, D., et al. (2012). Line-scanning particle image velocimetry: an optical approach for quantifying a wide range of blood flow speeds in live animals. PLoS One, 7(6), e38590. https://doi.org/10.1371/journal.pone.0038590.
Gao, Y. R., & Drew, P. J. (2014). Determination of vessel cross-sectional area by thresholding in Radon space. Journal of Cerebral Blood Flow and Metabolism, 34(7), 1180–1187. https://doi.org/10.1038/jcbfm.2014.67.
Ellefsen, K. L., Settle, B., Parker, I., & Smith, I. F. (2014). An algorithm for automated detection, localization and measurement of local calcium signals from camera-based imaging. Cell Calcium, 56(3), 147–156. https://doi.org/10.1016/j.ceca.2014.06.003.
Mukamel, E. A., Nimmerjahn, A., & Schnitzer, M. J. (2009). Automated analysis of cellular signals from large-scale calcium imaging data. Neuron, 63(6), 747–760. https://doi.org/10.1016/j.neuron.2009.08.009.
Stobart, J. L., Ferrari, K. D., Barrett, M. J. P., Stobart, M. J., Looser, Z. J., Saab, A. S., et al. (2016). Long-term in vivo calcium imaging of astrocytes reveals distinct cellular compartment responses to sensory stimulation. Cerebral Cortex. https://doi.org/10.1093/cercor/bhw366.
Pologruto, T. A., Sabatini, B. L., & Svoboda, K. (2003). ScanImage: flexible software for operating laser scanning microscopes. Biomedical Engineering Online, 2:13. https://doi.org/10.1186/1475-925X-2-13.
Linkert, M., Rueden, C. T., Allan, C., Burel, J. M., Moore, W., Patterson, A., et al. (2010). Metadata matters: access to image data in the real world. Journal of Cell Biology, 189(5), 777–782. https://doi.org/10.1083/jcb.201004104.
Dombeck, D. A., Khabbaz, A. N., Collman, F., Adelman, T. L., & Tank, D. W. (2007). Imaging large-scale neural activity with cellular resolution in awake, mobile mice. Neuron, 56(1), 43–57. https://doi.org/10.1016/j.neuron.2007.08.003.
Dabov, K., Foi, A., Katkovnik, V., & Egiazarian, K. (2007). Image denoising by sparse 3-D transform-domain collaborative filtering. IEEE Transactions on Image Processing, 16(8), 2080–2095. https://doi.org/10.1109/Tip.2007.901238.
Danielyan, A., Wu, Y. W., Shih, P. Y., Dembitskaya, Y., & Semyanov, A. (2014). Denoising of two-photon fluorescence images with block-matching 3D filtering. Methods, 68(2), 308–316. https://doi.org/10.1016/j.ymeth.2014.03.010.
Makitalo, M., & Foi, A. (2013). Optimal inversion of the generalized anscombe transformation for poisson-gaussian noise. IEEE Transactions on Image Processing, 22(1), 91–103. https://doi.org/10.1109/Tip.2012.2202675.
Acknowledgements
The authors are grateful to the many colleagues and collaborators who have provided feedback, suggestions and testing during the development process; to Rachel Barrett for assistance with documentation; and to the many developers who have made versions of their code and/or algorithms available. MJPB and JLS received funding from the University of Zurich Forschungskredit. JLS received funding from the Heart and Stroke Foundation of Canada. BW is a member of the University of Zurich Clinical Research Priority Program on Molecular Imaging.
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Conflict of Interest
The authors declare that they have no conflict of interest.
Rights and permissions
About this article
Cite this article
Barrett, M.J.P., Ferrari, K.D., Stobart, J.L. et al. CHIPS: an Extensible Toolbox for Cellular and Hemodynamic Two-Photon Image Analysis. Neuroinform 16, 145–147 (2018). https://doi.org/10.1007/s12021-017-9344-y
Published:
Issue Date:
DOI: https://doi.org/10.1007/s12021-017-9344-y