Title: Data from: Video-rate raman-based metabolic imaging by airy light-sheet illumination and photon-sparse detection
	Dataset DOI: 10.11578/1908656

Data, code and/or products within this dataset support the follwoing manuscript: 
	Manuscript Title: Video-rate raman-based metabolic imaging by airy light-sheet illumination and photon-sparse detection 
	Journal: PNAS
	DOI: 10.1073/pnas.2210037120 

Description/Abstract:
	Data supporting manuscript submitted to PNAS: Video-Rate Raman-based Metabolic Imaging by Airy Light-Sheet Illumination and Photon-Sparse Detection. The data set includes: [1] raw data and [2] related images used in the analyses described within the manuscript.

	Despite its massive potential, Raman imaging represents just a modest fraction of all research and clinical microscopy to date. This is due to the ultralow Raman scattering cross-sections of most biomolecules that impose low-light or photon-sparse conditions. Bioimaging under such conditions is suboptimal, as it either results in ultralow frame rates or requires increased levels of irradiance. Here, we overcome this tradeoff by introducing Raman imaging that operates at both video rates and 1,000-fold lower irradiance than state-of-the-art methods. To accomplish this, we deployed a judicially designed Airy light-sheet microscope to efficiently image large specimen regions. Further, we implemented subphoton per pixel image acquisition and reconstruction to confront issues arising from photon sparsity at just millisecond integrations. We demonstrate the versatility of our approach by imaging a variety of samples, including the three-dimensional (3D) metabolic activity of single microbial cells and the underlying cell-to-cell variability. To image such small-scale targets, we again harnessed photon sparsity to increase magnification without a field-of-view penalty, thus, overcoming another key limitation in modern light-sheet microscopy.

	**Data Use**:
	*License*: [CC-BY 4.0](https://creativecommons.org/licenses/by/4.0/)
	*Recommended Citation*: Vasdekis AE (2023) Data from: Video-rate raman-based metabolic imaging by airy light-sheet illumination and photon-sparse detection [Dataset]. University of Idaho. https://doi.org/10.11578/1908656

Resource URL: https://data.nkn.uidaho.edu/dataset/data-video-rate-raman-based-metabolic-imaging-airy-light-sheet-illumination-and-photon

Creator(s):	
	1. Full Name: Andreas E. Vasdekis 
		Unique identifier: https://orcid.org/0000-0003-4315-1047
		Affiliation(s): University of Idaho

Other Contributor(s): NULL

Publisher: University of Idaho

Publication Year: 2023

Language(s): American English

Subject(s): 
	1. NATURAL SCIENCES
		1.3 Physical Science
		1.6 Biological Science

Keywords/Tags: Raman imaging, photon-sparse imaging, light-sheet microscopy

Resource Type General: Dataset

Dates: NULL	

Date available for the public: 2023-02-22

Sizes: 273.9 MB

Format(s): Compressed data deirectory (zip) with txt, csv and tiff files. 

Version: NULL

Funding References: 
	U.S. Department of Energy
		Award: DE-SC0022282
		URL: NULL
		Title: Integrative Imaging of Plant Roots during Symbiosis with Mycorrhizal Fungi

Spatial/Geographical Coverage Location: NULL

Temporal Coverage: NULL

Granularity of the Data: NULL

Contact Info:
	Contact Name: Andreas Vasdekis
	Contact Email: andreasv@uidaho.edu

Related Content:
	Peer-reviewed manuscript-PNAS | https://doi.org/10.1073/pnas.2210037120 
	Project associated code-GitHub | https://github.com/aevasdekis/photon-sparse#photon-sparse

Data Files: 
	readme.txt
	Figure 4: file directory containing data files necessary to compile figure 4 of associated manuscript
		Figure_4a.csv: data for compiling the histogram presented in figure 4a 
			cell: ID of the cell observed
			sig_D2O: intensity values of a single cell grown in D2O
			bg_D2O: intensity values of background in D2O
			sig-bg_D2O: intensity difference between signal and background for a single cell grown in D2O
			sig_H2O: intensity values of a single cell grown in H2O [data only available for 1st 10 rows of data (cells h1-h10)]
			bg_H2O: intensity values of background in H2O [data only available for 1st 10 rows of data (cells h1-h10)]
			sig-bg_H2O: intensity difference between signal and background for a single cell grown in H2O [data only available for 1st 10 rows of data (cells h1-h10)]
		Figure_4b.csv: data for compiling the time-trace presented in figure 4b 
			time_min: temporal axis values (in sec)
			cell: intensity values for a single cell grown in D2O
			cell_norm: intensity values for a single cell grown in D2O, normalized at t = 1 min
	Figure 5: file directory containing data files necessary to compile figure 5 of associated manuscript
		220121_cloud_40x_90pct_focus.tif: 3D tif stack (xyt) representing single photon clouds as a function of time (t) of a single cell at focus
		Figure_5_error_analysis.csv: data of cell area error value represented in the insets of figure 5 
			photons-per-voxel: number of photons per unit voxel
			xy-area: cell area in the x-y plane in pixel units
			xy-area-per_norm: cell area in the x-y plane in pixel units normalized at 10 photons per voxel
			xz-area: cell area in the x-z plane in pixel units	
			xz-area-per_norm: cell area in the x-z plane in pixel units normalized at 10 photons per voxel
	Figure 6: file directory containing data files necessary to compile figure 6 of associated manuscript
	 	cell_1x1_figure_6a.tif: 2D tif image of a Y. lipolytica cell (as per Fig. 5) under pixel-level projection
		cell_2x2_figure_6b.tif: 2D tif image of a Y. lipolytica cell (as per Fig. 5) under sub-pixel projection
		Figure_6_traces.csv: data for compiling the traces presented in the insets of figure 6a and 6b
			Header Key:
				distance-pixel: x-axis distance in pixel units
				distance-μm: x-axis distance in micron units
				trace_1x1: trace of the Y. lipolytica cell under pixel-level projection
				trace_2x2: trace of the Y. lipolytica cell under sub-pixel projection