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. |