Detect spots over time on kymographs

1. Detect spots

The detection of spots on kymographs is done using the same principle as the detection of centrosomes: we search for local maxima on a prefiltered image.

Here, the spot prominence parameter is a factor. The base prominence is individually computed for each kymograph and is equal to the standard deviation of the pixel values on the kymograph. The final prominence is this base prominence multiplied by the spot prominence factor. The base value is 1.0 (since it is a factor) and the higher the factor, the less spots will be detected.

Spots will be displayed as gray circles on each kymograph.

_images/detected_spots.png

The gray circles are the detected spots on the kymographs.

2. Export the results

a. Export summary

The first thing that you can export is a summary of the number of events per point of time per kymograph. The produced file is a CSV file. All the columns start with either T or Count.

  • T is the index of the time point at which the event occured.

  • Count is the number of events that occured at this time point on this kymograph.

The second part of each column name is an expression of the form [PXX -> cYY] with XX being the ID of the pair and YY being the ID of the centrosome.

_images/spreadsheet.png

This is a screenshot from LibreOffice Calc in which the CSV was opened.

b. Export archive

In order to keep track of all the results, you can export an archive containing all the kymographs by clicking on the “Export archive” button. You will be asked a folder into which the ZIP archive will be created.

You can re-open this archive whenever you want. To do so, you have to:

  • Open Napari and open the “Nucleation analyzer” plugin.

  • Open again the image that you analyzed

  • Drag and drop the ZIP archive into the Napari viewer.

It should restore the whole process for visualization only, you cannot use that as a starting point to continue the analysis.

3. Analyze the next image

To reset your workspace and analyze another image, you can:

  1. Click on any layer in your layers list, press Ctrl + A to select all layers, then click on the trash can icon to delete all layers.

  2. In the “Pair tracks” sub-section of the plugin, click on the “Clear all” button to reset all the hints.