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

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.


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.


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

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