Design of a Line-of-Sight Fluorescence-Based Imaging Diagnostic for Classification of Microbe Species

This data set contains corrected two-color fluorescence intensity image data from 44 bacterial smears presented in the associated journal article, along with summary statistics, fluorescence spectra, and fluorescence intensity ratio histograms.

Article: Herzog et al 2023 Meas. Sci. Technol. https://doi.org/10.1088/1361-6501/acd711

The individual files are as files:

Corrected two-color fluorescence image data

B.cereus.tif

B.subtilis.tif

E.coli.tif

M.luteus.tif

Mold.tif

P.fluorescens.tif

R.rubrum.tif

S.marcescens.tif

Each file contains three-channel, 16-bit per sample image stacks. The Red and Blue image channels contain the corrected Red- and Blue-band fluorescence intensity data, respectively. Images were registered and corrected for LED intensity profile variation before storing. Each image corresponds to a different microbial smear. Image data is stored as 16-bit integers, although the raw data range is only 10-bit; typical intensity values are on the order of 1000.

It is recommended that ImageJ or a similar viewer be used to view the red and blue color channels independently with an appropriate scale.

Summary data

Summary.xlsx

This file contains a table of summary statistics from each of the 44 analyzed microbial smears. The columns are as follows:

Species: Name of the microbial species

Exposure: Exposure duration (UV LED and camera) in ms

Ratio: Most common ratio value (i.e., the mode of the ratio histogram)

Red: Median corrected red-band fluorescence intensity in counts

Blue: Median corrected blue-band fluorescence intensity in counts

R_fwhm: Full-width at half maximum of the ratio PDF

sR: Standard deviation of the corrected red-band fluorescence intensity in counts

sB: Standard deviation of the corrected blue-band fluorescence intensity in counts

R0: Median raw red-band fluorescence intensity in counts

B0: Median raw blue-band fluorescence intensity in counts

sR0: Standard deviation of the raw red-band fluorescence intensity in counts

sB0: Standard deviation of the raw blue-band fluorescence intensity in counts

Histogram data

Histogram.csv

Comma-separated histogram data, smoothed using a 7-bin wide 2nd order Savitzky-Golay filter. Each histogram is stored as a separate block with the format:

[Name]

[Comma-separated ratio bin values]

[Comma-separated smoothed count values]

Spectroscopy data

Spectra.csv

Comma-separated fluorescence spectra data, smoothed using a 10.5 nm wide 1st order Savitzky-Golay filter. Data was corrected for background and relative spectral response, then normalized by its integral and scaled by a factor of 100. Each histogram is stored as a separate block with the format:

[Species name]

[Comma-separated wavelength values]

[Comma-separated normalized corrected intensity values x 100]