Is TP1 the worm inside the egg or the worm outside the egg?

[ancneagu]

After the annotation is done, the images still show as the first image the worm inside the egg. While actually the first frame should be the first timepoint the worm is out of the egg. Is in the plotting, timepoint 1 the first frame the worm is outside the egg, or just like in the images, the worm still in the egg?

[imagejan]

The values in selection.csv contain the annotated start_t and end_t values.

When converting, the files are filtered according to their timepoint here:

ggrossha_SWI/source/s01_convert_to_zarr/run.py

Lines 306 to 307 in de528dc

	subset = subset[subset["time"] >= start_t]
	subset = subset[subset["time"] <= end_t]

The timepoint in turn - during annotation - is collected from the slider position here:

ggrossha_SWI/source/s01_convert_to_zarr/create_selection_csv_utils.py

Lines 119 to 121 in de528dc

	self.start_end_times[self.viewer.layers[0].name]["start_t"] = (
	self.viewer.dims.current_step[0]
	)

The mismatch likely is caused by the slider position being 0-based while the timepoint index in the filenames is 1-based.

The plotting just takes the time values on the x axis:

ggrossha_SWI/source/s03_measure/Plot_Results.ipynb

Line 201 in de528dc

"ax = sns.lineplot(included_measurements, x=\"time\", y=\"mean_intensity\", hue=\"condition\")\n",