Frequently asked questions

Approximate localization of molecules

What is "Peak intensity threshold" and what are the units?
This can be a number or a mathematical expression, see the threshold documentation. The units are A/D counts but note that the threshold is applied to the filtered image! Use the preview button in Run Analysis → Preview to see the filtered image and its values.

Message "Camera base level is set higher than values in the image!" during the data analysis.
This is just a warning that the camera base level (digitizer offset) is set too high. For such a frame, a minimum intensity value of the current image is subtracted from the image instead of using the value specified in the camera setup. Data are processed but the estimated photon count will be probably wrong. Please, set the camera base level according to the specification sheet supplied by the camera manufacturer.

Histogram of variables seems to be empty.
Automatic binning uses minimum and maximum value of the variable. This might not work if there are outliers. Try to use manual binning instead.

How to display/export only molecules around a specified center?
Use a filter rule with definition of a disc, e.g., (x-10000)^2 + (y-10000)^2 < 2000^2.

Regular grid artefacts in the image?
These are false positive detections. To remove them, use higher threshold value for approximate localization of molecules and process the data again, or use a filter post-processing to remove molecules with small sigma and high intensity.
Image coordinates shown in ImageJ vs. x and y columns shown in the table with localization results.
These coordinates match only if Left top x = 0 and Left top y = 0 in the Visualization ROI setup.
What is visualized?
This depends on what post-processing steps were applied. Visualized are values in the current table with localization results.

CSV
This is a text file with comma separated values. For import/export with, e.g., MS Excel, please make sure that the system localization settings use a point to separate decimal numbers (not comma as it is in some countries) and that comma is used to separate numbers.
XLS
This is a text file with values separated by a tabulator and not a MS Excel spread sheet.
What is exported?
This depends on what post-processing steps were applied. Exported are values in the current table with localization results.
Message "X and Y columns not found in Results table...." during the results import.
Colum names are case sensitive. Make sure that columns x and y (small letters) are present in the file header.

Due to recent changes on Google Drive, previous versions of ThunderSTORM (<1.3) cannot be updated automatically using the build-in updater. This has been fixed but you need to install the latest stable version manually.