TECHNICAL REPORT DEPT BME FMMU py oopsi the python…技术报告.pdfVIP

TECHNICAL REPORT, DEPT. BME, FMMU, 2014 1 py-oopsi: the python implementation of the fast-oopsi algorithm Benyuan Liu1 4 1 0 2 Abstract y a M Fast-oopsi was developed by joshua vogelstein in 2009, which is now widely used to extract neuron spike activities from calcium fluorescence signals. Here, we propose detailed implementation of the 6 fast-oopsi algorithm in python programming language. Some corrections are also made to the original ] E fast-oopsi paper. C . s c Index Terms [ 1 python, fast-oopsi, spikes, calcium fluorescence, connectomics v 1 8 1 I. FAST-OOPSI, A BRIEF VIEW 6 . 5 Oopsi, from vogelstein [1], [2], is a family of optimal optical spike inference algorithms. Here, we 0 4 focus on the development of the fast-oopsi, which was originally published in [2]. We will port the 1 : MATLAB implementation to python. Sec II, III, IV, V and VI are digests from the original paper by v i X vogelstein [1]. r The python implementation, py-oopsi, can be obtained at /liubenyuan/py-oopsi. a II. CALCIUM FLUORESCENCE MODEL Let F be a one-dimensional fluorescence trace. At time t, the fluorescence measurement Ft is a linear Gaussian function of the intracellular calcium concentration [Ca2+]t at that time: 2+ 2