trackmate-sc / trackmate-csvimporter Goto Github PK

Reported by Jeff-Gui, see https://forum.image.sc/t/spot-editing-failure-when-track-information-imported-by-trackmate-csv-importer/41775

The import processes as expected (see images below),but indeed, the spots are not editable anymore.
It is as if the image window was not registered by TrackMate.

With the new update of TrackMate (7.7.1) some dependencies seems to have been broken.

The Importer TrackMateImporter.java tries to access (line 510)

settings.xstart = 0;

but the settings value seems to be absent and I get following error

at fiji.plugin.trackmate.importer.csv.TrackMateImporter.createSettingsFromImageFile(TrackMateImporter.java:510) at fiji.plugin.trackmate.importer.csv.TrackMateImporter.createSettingsFromImageFile(TrackMateImporter.java:465) at fiji.plugin.trackmate.importer.csv.TrackMateImporter.getSettings(TrackMateImporter.java:204) at fiji.plugin.trackmate.importer.csv.TrackMateImporter.saveTo(TrackMateImporter.java:138) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) java.lang.NoSuchFieldError: java.lang.NoSuchFieldError: xstart

I've been trying to localize single molecules with ThunderSTORM and then pass these coordinates to TrackMate to do the tracking (file: 220322_slide2_1_tSTORM.csv). But, I found that the csv file that's directly exported from ThunderSTORM can't be read by TrackMate CSV Importer. In the Import log, I get:

Parsing records.
Could not parse line 1. Malformed number, skipping.
For input string: "1.0" Could not parse line 2. Malformed number, skipping.
For input string: "1.0" Could not parse line 3. Malformed number, skipping.

...and so on for every line of the csv file.

I had a look at a previous discussion on a similar subject: https://forum.image.sc/t/sptpalm-using-thunderstorm-and-trackmate/26039. From that forum, I downloaded the csv file that user had shared (Trial1.csv) to have a look. This one imported completely fine, with no error!

When looking carefully at the two csv files (mine and Trial1.csv), they look like they have an identical format at first. But, @HoldenLab noticed one very subtle difference: in Trial1.csv, the columns for "id" and "frame" are integers, while in mine they are floating points.

I converted those two columns to integers via Matlab (as that's what I'm most familiar with), and then the file uploads perfectly well with the CSV Importer.

So, it seems to be a simple issue. Maybe something changed with how ThunderSTORM exports csv files? At any rate, it would be most helpful if the Importer can read the csv file that's outputted straight from ThunderSTORM without needing to reformat it.

For further context, here is some further information that is possibly relevant:

• OS: Windows 10
• FIJI/ImageJ: v1.53q
• ThunderSTORM: v1.3?
• TrackMate CSV Importer: v.3.1.1