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Opening a Dataset

Importing data is one of the most important aspects of this plugin. All the supported formats can be easily opened using Drag and Drop onto the napari window, or with File>Open File(s).... If there is no available data, the user may use one of the sample datasets the plugin comes with: File>Open Sample>ReLAX>demo lineageTree dataset or C. elegans dataset (see Quick Start).

1. Check the Format

Format Extension Notes
LineageTree .lT Native format. Also stores the labels and comparisons made in ReLAX.
MaMuT or ASTEC .xml ReLAX asks which of the two tools produced the file.
Mastodon .mastodon Mastodon project file.
BMF .bmf

LineageTree can read more formats, for example CSV, TGMM XML or SWC files. To open one of them in ReLAX, convert it to .lT first:

from lineagetree import read_from_csv

lT = read_from_csv("tracks.csv")
lT.write("tracks.lT")

The LineageTree loaders documentation lists all readers and their options.

2. Choose the Loader (.xml only)

When several loaders can read the file, a lineagetree data type selection window asks the user to select the method used to produce the dataset. Tick the tool that produced the file: MaMuT XML loader or ASTEC XML loader. Closing the window without choosing stops the import.

3. Set the Loading Parameters

Every file then opens a Loading Parameters window:

  • Time resolution (mins): the time between two consecutive timepoints, pre-filled with the value stored in the dataset. The Manager uses it to align datasets acquired at different rates.
  • Resave dataset with new time resolution: writes the dataset with the new time resolution as a .lT file. An opened .lT file is overwritten; for other formats, .lT is added to the file name (embryo.xml becomes embryo.xml.lT).
  • Rescale Dataset: divides all positions by the largest distance between two cells of the dataset, so that datasets with different spatial units appear at a similar scale.
  • Filter Dataset: hides small lineages from the Lineage Viewer. With a value n above 0, only lineages with at least (number of timepoints) / n nodes are listed; 0 keeps every lineage. All cells are still shown in the napari viewer.

Press Ok to load the dataset or Cancel to abort.

4. Start Exploring

Loading a dataset adds:

  • a Points layer named after the file, with one point per cell and timepoint, colored by lineage;
  • a Surface layer named <file name>_mesh if the dataset contains cell meshes. It is linked to the Points layer.

Select the Points layer and open Plugins>Lineage tree analysis to explore it with the Lineage Viewer.

Troubleshooting

  • The file is not offered to ReLAX: check that its extension is one of the supported ones above, or convert it to .lT.
  • "Please select one reader function.": the loader window was closed without choosing a loader. Open the file again and tick one.
  • Ok does nothing in the Loading Parameters window: the time resolution must be a number.