GoFigure eXchange format

A description of the file format for passing segmentation and tracking results from any stand alone application to GoFigure. These files are then used to fill the database.

1. Segmentation Results

1.1 The name of the files

  • Since most of segmentation algorithm work on one time point, one text file must be created for each time point.
  • For example results from 3 time points, we have 3 text files: 0.txt, 1.txt and 2.txt. Note that the file name does not really matter as long as it is clear to which time point it corresponds.
  • If the segmentation process work on several time point, the file format can handle it. However for the sake of clarity specify in the file name which time point are present in the file.

1.2 The content of the current files

  • First let's consider we have one file mesh0.txt (result of the segmentation process for the time point 0).
  • The size depends on the number of meshes we have.
  • Please note that "TCoord" must be the same as the text file we are working in:
    • Mesh0.txt -> TCoord 0
    • Mesh1.txt -> TCoord 1
    • ...
<ImagingSession>                             |   **** SESSION INFORMATIONS ****
HeaderFile CaltechZebrafishSubsetData.meg | Name of the MegaCaptureFile containing all the imaging session information
</ImagingSession> |
<mesh> | **** MESH INFORMATIONS ****
TrackId 1 | + Id of the track that the mesh belongs to
TCoord 0 | + Time coordinate of the mesh
Centroid 114.4960 202.7230 66.7290 | + Spatial coordinate of the mesh
Volume 537.92 | + Size of the mesh (in um^3)
Filename 0_1.vtk | + Corresponding .vtk file
<intensity> | + intensity informations (number of intensity information depends on the imaging session)
Channel 0 | - Channel Number
AverageValue 95.95 | - Average intensity for the corresponding channel
</intensity> |
<intensity> |
Channel 1 |
AverageValue 185.76 |
</intensity> |
<intensity> |
Channel 2 |
AverageValue 0.00 |
</intensity> |
</mesh> |
<mesh> | **** MESH INFORMATIONS ****
TrackId 2 | + Id of the track that the mesh belongs to
...
</mesh> |
...

2. Tracking Results

2.1 The content of the files

<ImagingSession>                             |   **** SESSION INFORMATIONS ****
HeaderFile CaltechZebrafishSubsetData.meg | Name of the megaFile containing all the session information
</ImagingSession> |
NumberOfTracks 327 | Number of tracks contained in the lineage
<Track> | **** TRACK INFORMATION ****
LineageID 0 | + Id of the lineage that the track belongs to
<ListOfMeshes> | **** GLOBAL MESH INFORMATIONS ****
NumberOfMeshes 23 | + Number of meshes contained in the track
<mesh> | **** MESH INFORMATIONS ****
TrackId 1 | + Id of the track that the mesh belongs to '''Is it really required since they all belong to the same track?'''
TCoord 0 | + Time coordinate of the mesh
Centroid 114.4960 202.7230 66.7290 | + Spatial coordinate of the mesh
Volume 537.92 | + Size of the mesh
Filename 0_1.vtk | + Corresponding .vtk file
<intensity> | + intensity informations
Channel 0 | - Channel
AverageValue 95.95 | - Average corresponding intensity
</intensity> |
<intensity> | + intensity informations
Channel 1 | - Channel
AverageValue 185.76 | - Average corresponding intensity
</intensity> |
<intensity> | + intensity informations
Channel 2 | - Channel
AverageValue 0.00 | - Average corresponding intensity
</intensity> |
</mesh> |
<mesh> | **** MESH INFORMATIONS ****
TrackId 2 | + Id of the track that the mesh belongs to
... |
</mesh> |
... |
</ListOfMeshes> |
... |
</Track> |
... |
<Track> |
... |
</Track> |