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BaF3: add TrackMate data #18

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merged 3 commits into from
Apr 17, 2017
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simleo
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@simleo simleo commented Apr 5, 2017

Adds tracking data from TrackMate, generated by @pcmasuzzo. The only differences with the original datapackage are:

  • dp.json renamed to datapackage.json
  • altered some names in the above file to make it compliant with the specs (see Spec compliance biotracks#3)

Opening this mainly for discussion re: standardization, since I've found it awkward to modify the overlay notebook to accommodate for multiple packages. Specifically, see the time_col, x_col, etc. mappings: we wouldn't need these if we included in our version of the format a standard way to refer both to tabular file names and to column names within them. We can either agree on fixed names for all these entities or add a level of indirection, i.e., something like the .ini file currently used to generate datapackages in https://github.com/CellMigStandOrg/cell_track_dpkg. However, since the file containing name mappings would have to be itself included in the package, we should probably hardwire file names and use mappings only for column names.

The other issue is that TrackMate object coordinates are in physical size (µm in this case), so I had to retrieve the scaling factor from the metadata and apply it to the plot in order to make things match. The standard should either expect pixel-based XY coordinates that directly map to the images (meaning the datapackage generator should ensure this) or support some way of expressing any required conversion.

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sbesson commented Apr 17, 2017

Overall, 👍 for working from multiple examples rather than one (as it forces us to consider the standardization of fields). Merging this and I will comment on the issue separately.

@sbesson sbesson merged commit 24e6cdc into CellMigStandOrg:master Apr 17, 2017
@simleo simleo deleted the baf3_trackmate branch April 17, 2017 15:20
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