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Database contents

Legend:

  • Mol*VS ID: unique identifier for the entry in the Mol*VS internal database. Links to pre-made visualization if available.
  • Source data: original data set. We source all EMDB and EMPIAR entries with segmentation data. Additionally, we have included several examples to indicate that Mol*VS is prepared to handle application-specific segmentation data (.am, .mod, .seg, .stl) in addition to formats promoted by public databases.
  • Notes: context about how data were obtained or processed
  • Known issues: context about known problems or limitations of specific entries

Sourced from EMDB

Mol*VS ID Source data Notes Known issues
emd-1014 EMD-1014
emd-1080 EMD-1080
emd-1181 EMD-1181
emd-11810002 EMD-1181 Same as emd-1181 but with custom segmentation computed by Amira.
emd-1547 EMD-1547
emd-1832 EMD-1832
emd-1963 EMD-1963
emd-20293 EMD-20293
emd-2847 EMD-2847
emd-5143 EMD-5143
emd-5250 EMD-5250
emd-6338 EMD-6338
emd-90940001 EMD-9094 Source dataset does not contain segmentations, so volume segmentation was performed in house using IMOD and the output was internally converted to EMDB-SFF using sfftk. The segments have not been evaluated for their biological relevance. This entry was added to showcase the support for application-specific segmentation formats.
emd-90940002 EMD-9094 Source dataset does not contain segmentations, so volume segmentation was performed in house using Segger and the output was internally converted to EMDB-SFF using sfftk. The segments have not been evaluated for their biological relevance. This entry was added to showcase the support for application-specific segmentation formats.

Sourced from EMPIAR

Mol*VS ID Source data Notes Known issues
empiar-10070 [EMPIAR-10070] - B3TALONGMUSC20130301 - -
empiar-1008702 [EMPIAR-10087] - C2_TOMO02 Segment with id 22 has no segmentation data, name, or description and was therefore not processed
empiar-1008703 [EMPIAR-10087] - E64_TOMO03 -
empiar-10819 [EMPIAR-10819] - MP014_EM04468_2_8T_CROP_XZ_ROTATED-20NM Source dataset does not contain segmentations. If default settings do not render anything, turn GPU support off and use a negative isovalue, or use direct volume render and adjust the control points.

Sourced from IDR

Mol*VS ID Source data Notes Known issues
idr-6001240 [idr0062-blin-nuclearsegmentation/experimentA] - B1_C1.tiff Nuclear segmentation image of mouse blastocysts under confocal microscopy If default settings do not render anything, turn GPU support off (if using Isosurface) or just use Direct volume.