Welcome

Open Fiber Photometry

The three-dimensional signal collection field for
fiber photometry in brain tissue

Marco Pisanello1,†,*, Filippo Pisano1,†, Minsuk Hyun2,†, Emanuela Maglie1,3, Antonio Balena1,3, Massimo De Vittorio1,3, Bernardo L. Sabatini2,*, and Ferruccio Pisanello1,*

1 Istituto Italiano di Tecnologia (IIT), Center for Biomolecular Nanotechnologies (CBN), Italy.
2 Department of Neurobiology, Howard Hughes Medical Institute, Harvard Medical School, U.S.A.
3 Dipartimento di Ingegneria dell’Innovazione, Università del Salento, Italy.

 These authors have contributed equally to this work.

* Correspondence to: Marco Pisanello (marco.pisanello@iit.it), Bernardo L. Sabatini (bernardo_sabatini@hms.harvard.edu), Ferruccio Pisanello (ferruccio.pisanello@iit.it).

Frontiers in Neuroscience, 13:82. doi: 10.3389/fnins.2019.00082.
 

If you reuse data, codes, or models from this webpage, please cite: M. Pisanello, F. Pisano, M. Hyun, E. Maglie, A. Balena, M. De Vittorio, B.L. Sabatini, and F. Pisanello. The three-dimensional signal collection field for fiber photometry in brain tissue. Front. Neurosci. 13:82 (2019). doi: 10.3389/fnins.2019.00082.
 

RAW DATA

Click here to download collection fields in quasi transparent fluorescent medium. Within the zip archive you’ll find raw data (microscope and fiber acquired tiff stacks and results from ray-tracing simulations) and Matlab code for their processing, organized in different folders by fiber NA (0.22, 0.39, and 0.50) and sample number (A, B, C, and D).

Click here to download collection fields in fluorescently stained brain slice. Within the zip archive you’ll find raw data (microscope and fiber acquired tiff images) and Matlab code for their processing, organized in different folders by fiber NA (0.39 and 0.50) and sample number (A, B, and C).

Click here to download photometry efficiency in fluorescently stained brain slice. Within the zip archive you’ll find raw data (non de-scanned microscope and fiber acquired tiff images and through de-scanned pinhole images) and Matlab code for their processing, organized in different folders by fiber NA (0.39 and 0.50).

ZEMAX MODEL

Click here to download Zemax models for determining light collection fields in homogeneous and scattering medium. Within the zip archive you’ll find the Zemax lens models (zmx files) and macros (zpl files), and a guidelines document.

MATLAB FUNCTIONS

Click here to download the definition of Matlab functions required from the processing scripts.

 

 

 

Influence of anatomical features of different brain regions on the spatial localization of fiber photometry signals

Cinzia Montinaro1,2,*, Marco Pisanello1, Marco Bianco1,3, Barbara Spagnolo1, Filippo Pisano1, Antonio Balena1, Francesco De Nuccio2, Dario Domenico Lofrumento2, Tiziano Verri2, Massimo De Vittorio1,3,*, †, and Ferruccio Pisanello1, *,†

1 Istituto Italiano di Tecnologia (IIT), Center for Biomolecular Nanotechnologies (CBN), Italy
2 Dipartimento di Scienze e Tecnologie Biologiche e Ambientali, Università del Salento, Lecce, Italy
3 Dipartimento di Ingegneria dell’Innovazione, Università del Salento, Italy.

† These authors have contributed equally to this work.
* Correspondence to: Cinzia Montinaro (cinzia.montinaro@iit.it), Massimo De Vittorio (massimo.devittorio@iit.it), Ferruccio Pisanello (ferruccio.pisanello@iit.it).

This paper has been published in Biomedical Optics Express. doi: https://doi.org/10.1364/BOE.439848.
 

If you reuse data, codes, or models from this webpage, please cite:
C. Montinaro, M. Pisanello, M. Bianco, B. Spagnolo, F. Pisano, A. Balena, F. De Nuccio, D. D. Lofrumento, T. Verri, M. De Vittorio, and F. Pisanello. Influence of anatomical features of different brain regions on the spatial localization of fiber photometry signals. Biomed. Opt. Express (2021). doi: https://doi.org/10.1364/BOE.439848.

How to open the raw data

This zip folder contains all relevant data presented in the manuscript organized in different folders by figures (1, 2, 3, 4, 5) and supplementary figures (1, 2, 3).

For data concerning brain slices images, within the zip archive you’ll find raw data in .tiff format concerning:

  • f(x,y,z) , named bench.tiff

  • mu(x,y,z) , named top.tiff

  • beta (x,y) , named ill.tiff

  • background noise, named benchfondo.tiff

The best way to open .tiff files is to use ImageJ or Fiji.

Photometry efficiency fieds and other relevant informations including isolines, three-dimensional diagrams, axial intensity profiles and η(x,y) are computed through matlab scripts. All .m matlab scripts are commented, and to run them you need to first import the workspace.mat which is in the same folder of the .m file.

For other graphs, in the folder reffered to each panel, you will find a .txt file with detailed instruction on how to read the graph.