README_FlowCam_rawdata

Data package: Dataset for comparison of FlowCam and microscopy
Contact: Jasper Münnich, jasper.muennich1@gmail.com
Date created: 2026-04-28


File directory: group/
Description: The raw data directory 'group/' contains CSV files for each phytoplankton group found per sample using FlowCam (236 files, 30.2 MB). Each file contains the VisualSpreadsheet output for each detected particle per group.

Variable descriptions based on the Visual Spreadsheet User Guide (Yokogawa Fluid Imaging Technologies, Inc.).


Column name: Particle ID
Description: The particle identification number.

Column name: Area (ABD)
Description: Number of pixels in the threshold (binary) greyscale image converted to a measure of area by use of the calibration factor. Units = μm2. ABD = Area Based Diameter.

Column name: Area (Filled)
Description: The area represented by the particle edge and all the pixels inside the edge.

Column name: Aspect Ratio
Description: The ratio of the lengths of the axes of the Legendre ellipse of inertia of the particle.

Column name: Average Blue
Description: Average pixel value of the blue color plane.

Column name: Average Green
Description: Average pixel value of the green color plane.

Column name: Average Red
Description: Average pixel value of the red color plane.

Column name: Calibration Factor
Description: The conversion factor from pixels to microns (units are microns per pixel).

Column name: Calibration Image
Description: he number of the calibration image that was used in processing the particle.

Column name: Camera
Description: The camera number.

Column name: Capture X
Description: The leftmost X coordinate in pixels of the particle in the original image.

Column name: Capture Y 
Description: The top Y coordinate in pixels of the particle in the original image.

Column name: Ch1 Area
Description: Log10 (Area of fluorescence peak of photomultipler tube (PMT) #1).

Column name: Ch1 Peak
Description: Log10 (Peak fluorescence value read from PMT #1).

Column name: Ch1 Width
Description: Log10 (Width of PMT #1 above the threshold value).

Column name: Ch2 Area
Description: Log10 (Area of fluorescence peak of PMT #2).

Column name: Ch2 Peak
Description: Log10 (Peak fluorescence value read from PMT #2).

Column name: Ch2 Width
Description: Sample Log10 (Width of PMT #2 above the threshold value).

Column name: Ch2/Ch1 Ratio
Description: Log10 (Ch2 Peak) - Log10(Ch1 Peak).

Column name: Circle Fit
Description: Deviation of the particle edge from a best-fit circle, normalized to the range [0,1] where a perfect fit has a value of 1.

Column name: Circularity
Description: A shape parameter computed from the perimeter and the (filled) area.

Column name: Circularity (Hu)
Description: An alternative measure of circularity that often provides a better indication of the circular shape of a particle than does Circularity, especially if the particle is very small or its edge has defects.

Column name: Compactness
Description: A shape parameter derived from the perimeter and the (filled) area.
 
Column name: Convex Perimeter
Description: Perimeter of the convex hull.

Column name: Convexity
Description: A shape parameter that is computed as the ratio of filled area to the area of the convex hull of the particle.

Column name: Date
Description: Date of sample processing.

Column name: Diameter (ABD)
Description: The diameter based on a circle with an area that is equal to the ABD Area.

Column name: Diameter (ESD)
Description: The Mean value of 36 feret measurements. ESD = Equivalent Spherical Diameter.

Column name: Diameter (FD)
Description: The diameter based on a circle with an area (filled) that is equal to the Area (Filled). FD = Filled Diameter.

Column name: Edge Gradient
Description: Average intensity of the pixels making up the outside border of a particle after a Sobel Edge Detect convolution filter has been applied to the raw camera image.

Column name: Elapsed Time
Description: Time since the start of the run when this particle was found. Unit=seconds

Column name: Elongation
Description: The inverse of Geodesic Aspect Ratio.

Column name: Feret Angle Max
Description: Angle of the largest feret measurement.

Column name: Feret Angle Min
Description: Angle of the smallest feret measurement.

Column name: Fiber Curl
Description: A shape parameter computed from Geodesic Length and Length.

Column name: Fiber Straightness
Description: A shape parameter computed from Geodesic Length and Length.

Column name: Filter Score
Description: The statistical filter score.

Column name: Geodesic Aspect Ratio
Description: The ratio of Geodesic Thickness to Geodesic Length. Unit= μm

Column name: Geodesic Length
Description: Values obtained by modeling the particle as a rectangle and computing length. Unit= μm

Column name: Geodesic Thickness
Description: Values obtained by modeling the particle as a rectangle and computing width.

Column name: Image File
Description: The collage image filename that contains this particle.

Column name: Image Height
Description: The image height in pixels of the particle in the saved collage image. Unit=pixel

Column name: Image Width
Description: The image width in pixels of the particle in the saved collage image. Unit=pixel

Column name: Image X
Description: The left most X coordinate in pixels of the particle image in the saved collage image.

Column name: Image Y
Description: The top Y coordinate in pixels of the particle in the saved collage image.

Column name: Intensity
Description: The average grayscale value of the pixels making up a particle (grayscale sum / number of pixels making up the particle)

Column name: Length
Description: The maximum value of 36 feret measurements. Unit=μm

Column name: Original Reference ID
Description: NA

Column name: Particles Per Chain
Description: The number of particles that were grouped into one particle based on the nearest neighbor distance.

Column name: Perimeter
Description: The length of the particle edge not including the lengths of edges of holes in the particle. Unit=μm

Column name: Ratio Blue/Green
Description: Average Blue / Average Green.

Column name: Ratio Red/Blue
Description: Average Red / Average Blue.

Column name: Ratio Red/Green
Description: Average Red / Average Green.

Column name: Roughness
Description: A measure of the unevenness or irregularity of a particle’s surface-the ratio of perimeter to convex perimeter.

Column name: Scatter Area
Description: Area of the peak of the scatter detector measured over the width.

Column name: Scatter Peak
Description: Peak value read from the scatter detector. 

Column name: Scatter Width
Description: Sample width of scatter detector values above the scatter threshold.

Column name: Sigma Intensity
Description: Standard deviation of grayscale values.

Column name: Source Image
Description: The camera image number or raw file image number where the particle was captured.

Column name: Sphere Complement
Description: NA

Column name: Sphere Count
Description: NA

Column name: Sphere Unknown
Description: NA

Column name: Sphere Volume
Description: NA

Column name: Sum Intensity
Description: Sum of grayscale pixel values.

Column name: Symmetry
Description: A measure of the symmetry of the particle about its center.

Column name: Time
Description: The time that the image was captured.

Column name: Timestamp
Description: The time the image was captured in milliseconds.

Column name: Transparency
Description: 0 is the value for a filled circle; values near 1 are for an elongated or irregular shape or a shape that has many interior holes.

Column name: Volume (ABD)
Description: Sphere volume calculated from ABD Diameter. Unit=μm3

Column name: Volume (ESD)
Description: Sphere volume calculated from ESD Diameter. Unit=μm3

Column name: Width
Description: The minimum value of 36 feret measurements. Unit=μm
