Soma-io: Add ROIs parameters to header

[denisri]

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Author Name: Souedet, Nicolas (@nsouedet)
Original Redmine Issue: 14790, https://bioproj.extra.cea.fr/redmine/issues/14790
Original Date: 2016-05-09

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Openslide images (at least CZI files) contain meta information that describe scanned regions of the image.
Do you think that it would be relevant to add this ROIs information to the header ?
An example integration in header could be:

{
  'volume_dimension' : [ 1900, 1402, 1, 1 ],
  'resolutions_dimension' : [ [ 1900, 1402, 1, 1 ] ], 
  'voxel_size' : [ 0.0356863029301167, 0.0355775877833366, 1, 1 ],
  'object_type' : 'Volume',
  'data_type' : 'RGBA',
  'file_type' : 'OpenSlide',
  'rois' : [ { 'type': 'parallelepiped',
               'origin': [ 45.5, 30, 0, 0 ],
               'sizes': [10.4, 5.3, 1, 1] }, 
             { 'type': 'sphere',
               'center': [ 10.3, 7.9, 0, 0 ],
               'radius': 5.2 } ]
}

[denisri]

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Original Redmine Comment
Author Name: Riviere, Denis (@denisri)
Original Date: 2016-05-09T13:27:15Z

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Why not if you have such information. It can always fit in a .minf. The real trouble is to standardize and maintain the consistency of such information.

[denisri]

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Original Redmine Comment
Author Name: Cointepas, Yann (@sapetnioc)
Original Date: 2016-05-09T13:40:23Z

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In your example, I do not understand the meaning of each volume in "rois".
Is it just a series of parametric ROIs connected somehow to the image (i.e.
dependant of the context of creation and use of the image) ?

Yann Cointepas Tel: +33 1 69 08 78 31
CEA - Neurospin Fax: +33 1 69 08 79 80
Bâtiment 145, Point Courrier 156
91191 Gif-sur-Yvette cedex, France

On Mon, May 9, 2016 at 3:09 PM, [email protected] wrote:

La demande #14790 a été soumise par Souedet, Nicolas.

Request #14790: Soma-io: Add ROIs parameters to header
https://bioproj.cea.fr/redmine/issues/14790

• Auteur: Souedet, Nicolas
• Statut: New
• Priorité: Normal
• Assigné à:
• Catégorie: soma-io
• Version cible: soma-trunk

Openslide images (at least CZI files) contain meta information that
describe scanned regions of the image.
Do you think that it would be relevant to add this ROIs information to the
header ?
An example integration in header could be:

{
'volume_dimension' : [ 1900, 1402, 1, 1 ],
'resolutions_dimension' : [ [ 1900, 1402, 1, 1 ] ],
'voxel_size' : [ 0.0356863029301167, 0.0355775877833366, 1, 1 ],
'object_type' : 'Volume',
'data_type' : 'RGBA',
'file_type' : 'OpenSlide',
'rois' : [ { 'type': 'parallelepiped',
'origin': [ 45.5, 30, 0, 0 ],
'sizes': [10.4, 5.3, 1, 1] },
{ 'type': 'sphere',
'center': [ 10.3, 7.9, 0, 0 ],
'radius': 5.2 } ]
}

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[denisri]

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Original Redmine Comment
Author Name: Souedet, Nicolas (@nsouedet)
Original Date: 2016-05-09T14:19:02Z

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Yes it is just a series of parametric ROIs in the image.
The reality is that our scanner generate images that can be sparse and contain only data in some scanned ROIs.
The description of these ROIs can be interesting to use later in some processes.
Please, find attached an example of our data (transparent or black areas are areas that were not scanned).

[sapetnioc]

@nsouedet , what is the status of this issue ?