Spotfinder coordinates files

Spotfinder coordinates files are ASCII files with the extension .spots. They are usually found in the main/video_processing/coordinates/spotfinder analysis folder.

Table of contents

1. Description
2. File name
3. Structure
4. Compatibility

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Description

The spots coordinates file is written in ASCII format and contain pixel positions of bright spots detected with Spotfinder.

It is created in the /video_processing/coordinates/spotfinder analysis sub-folder when saving spots coordinates in panel Molecule coordinates of module Video processing.

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File name

The file is named by the user during the export process.

By default, the file is named after the image/video file name loaded in Video processing.

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Structure

Coordinates are written in double precision and are organized in a column-wise fashion with:

• columns x and y containing x- and y- spots coordinates respectively
• column I containing the pixel intensities at spots positions using Pixel intensity units
• column frame containing frame indexes on which the spot detection was performed

x		y		I	frame
1.450000e+01	3.450000e+01	518	1
7.350000e+01	2.150000e+01	542	1
1.350000e+01	1.405000e+02	547	1

In the case where the Method settings include Gaussian fitting, the column I contains Gaussian numeric integrals and the following columns and inserted:

• assymetry containing spot asymmetries in %, being equal of greater than 100%
• width and height containing Gaussian standard deviations in the x- and y- direction respectively and given in pixel
• theta Gaussian orientation in radian
• z-offset Gaussian offset given in Pixel intensity units

x		y		I		assymetry	width		height		theta		z-offset	frame
1.500000e+01	3.800000e+01	1.200463e+02	1.000000e+00	3.402311e-01	3.402311e-01	-3.230343e+04	1.129999e+03	1
1.033617e+02	1.942211e+02	1.212129e+02	1.162688e+00	8.045870e-01	6.920058e-01	-9.087937e+00	1.129771e+03	1
3.499995e+01	1.107173e+02	1.260142e+02	1.708943e+00	7.835743e-01	4.585141e-01	-1.169097e+05	1.129877e+03	1

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Compatibility

Spots coordinates files can be imported for coordinates transformation in panel Coordinates transformation by adjusting the corresponding Import options to the actual file structure