Processing data from two-photon microscope
| Thesis title in Czech: | Processing data from two-photon microscope |
|---|---|
| Thesis title in English: | Processing data from two-photon microscope |
| Key words: | dvoufotonový mikroskop, zobrazování, zpracování, segmentace |
| English key words: | two-photon microscope, imaging, processing, segmentation |
| Academic year of topic announcement: | 2012/2013 |
| Thesis type: | diploma thesis |
| Thesis language: | angličtina |
| Department: | Department of Theoretical Computer Science and Mathematical Logic (32-KTIML) |
| Supervisor: | Ondřej Novák |
| Author: | hidden - assigned and confirmed by the Study Dept. |
| Date of registration: | 09.11.2012 |
| Date of assignment: | 13.11.2012 |
| Confirmed by Study dept. on: | 27.11.2012 |
| Date and time of defence: | 15.05.2013 11:00 |
| Date of electronic submission: | 12.04.2013 |
| Date of submission of printed version: | 12.04.2013 |
| Date of proceeded defence: | 15.05.2013 |
| Opponents: | RNDr. Václav Krajíček, Ph.D. |
| Advisors: | doc. Mgr. Cyril Brom, Ph.D. |
| Guidelines |
| The method of in vivo two-photon microscopy and its application – calcium imaging – already provides important information about how neuronal networks work in vivo. However, analyzing all the data coming out of the microscope calls for automated software processing. There are existing publications describing partial software automatization of activity measurement of neurons in brain. Unfortunately, the published programs largely do not perform fast enough and they have problems with processing data from living animals (movement artifacts, lower SNR, etc.).
The aim of this thesis is to design and implement algorithms necessary for complex processing of in vivo data from two-photon microscope, capable of dealing with issues of recording from living animals. The solved tasks will be: Automated searching for neurons in TSeries mode (full-frame acquisition); automated searching for neurons in Linescan mode (scanning a pattern in an image); extraction of calcium traces of found neurons; possibly also further visualization of neuronal properties (i.e., receptive fields). Available published spike-mining algorithms will be used to detect action potentials in the calcium traces. A set of automated tests (using synthetic, easy to analyze data) will be performed on the software, testing its correctness. Evaluation of the TSeries neuron searching algorithm against other published algorithms solving the same task will be also a part of the thesis. Fast method for automated searching for neurons in TSeries mode will be the most important part of the thesis. The aim will be to make it fast enough to bring its performance as near as possible to real sampling frequency when recording data (20-30 FPS). Such a fast algorithm would allow researchers to target and manipulate neurons in real time. |
| References |
| Rothschild G., Nelken I., Mizrahi A.: Functional organization and population dynamics in the mouse primary auditory cortex. In: Nature Neuroscience 13, 353–360 (2010), doi:10.1038/nn.2484
Stosiek C., Garaschuk O., Holthoff K., Konnerth A.: In vivo two-photon calcium imaging of neuronal networks. In PNAS 2003 100 (12) 7319-7324; published ahead of print May 30, 2003,doi:10.1073/pnas.1232232100 Lütcke H., Helmchen F.: Two-photon imaging and analysis of neural network dynamics. In 2011 Rep. Prog. Phys. 74 086602 doi:10.1088/0034-4885/74/8/086602 Watson, C. et al.: The Mouse Nervous System. ISBN: 978-0-12-369497-3 |