CT data
- Doug Boyer
The table below gives a number of examples of derivative data that can be generated from CT projection series. These are not the only possibilities. Furthermore, "raw data" are never required and are often disallowed. For example, if a CT scan containing several different specimens was made, both the raw data and derivative data 1 would be disallowed. The projection series (raw data) would have to be reconstructed (derivative 1) and then cropped so that each volume represented a single specimen (derivative 2) before being uploaded. In such cases, at the beginning of the upload the user would simply indicate they had "derivative data" and that the raw data are "not available". They would then select "reconstruction" and "crop" as two processing activities that had been applied to the file they uploaded.
| Criteria | Raw data | Derivative data 1 | Derivative data 2 | Derivative data 3 | Derivative data 4 | Derivative data 5 |
|---|---|---|---|---|---|---|
| Importance for reproducibility and re-use | low | high-highest | high-highest | medium | medium | low |
| type | projection series | reconstructed image stack | cropped image stack | segmented mesh | segmented mesh with textures | image (screenshot) |
| formats | .tiff or other open, lossless raster | any open raster (preferably lossless) | any open raster (preferrably lossless) | any open format (obj, ply, stl, glb, gLTF) | (obj+mtl+texture); glb; (gLTF+texture); ply | any open raster |
| zip** files required/recommended/discouraged? | required | required | required | discouraged* | required when using obj+mtl+texture; note that neither ply or stl are compatible with textures | discouraged |
| critical metadata for accurate reuse | (1) source to object distance; (2) source to detector distance; (3) pixels in y direction; (4) pixels in x direction; (5) width of y pixels; (6) width of x pixels | voxel dimensions (x,y, and z directions); units of voxel dimensions (if other than millimeters) | voxel dimensions (x,y, and z directions); units of voxel dimensions (if other than millimeters) | units of mesh coordinates (if other than millimeters) | units of mesh coordinates (if other than millimeters) | none |
| attachments recommended | yes - log file from scanner as .txt or .pdf | yes (if no parent files included) - log file from scanner as .txt or .pdf | yes (if no parent files included) - log file from scanner as .txt or .pdf | yes (if no parent files included) - log file from scanner as .txt or .pdf | yes (if no parent files included) - log file from scanner as .txt or .pdf | na |
| Thumbnail*** | sample image from projection series | sample image from reconstructed image stack | sample image from cropped image stack | screenshot of segmented mesh | screenshot of segmented mesh with texture | na |
| Preview setting | Select "use 2D thumbnail" | Select "interactive preview" | Select "interactive preview" | Select "interactive preview" | Select "interactive preview" | na |
*"discouraged" means that the system does not prevent you from uploading a zip for the given derivative type, but mostly likely a member of the MorphoSource support team will eventually contact you and ask you to replace the zip with something else.
**zip files should never be created using OS archiving tools (instead, use freeware: Mac - Keka / PC - 7zip). Zip files should always be saved in .zip format.
***Thumbnails cannot be larger than 50mb in size or the system will reject them and notify you of the rejection.