Add some HiP-CT docs #18
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kabilar
reviewed
Sep 20, 2024
| The chunk number is set to `yyxx`, where yy is the resolution of the scan in micrometers, and xx is a scan number that is unique between datasets. | ||
| For example, a scan number of `402` is the second 4um scan. | ||
| The highest lowest resolution dataset (equivalently, highest chunk number) is the overview dataset that contains an image of the whole sample. | ||
| There are then one or more datsets at higher resolution. |
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| There are then one or more datsets at higher resolution. | |
| There are then one or more datasets at higher resolution. |
kabilar
reviewed
Sep 20, 2024
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| Datasets have the name `sub-<donor>_sample-<sample name>_chunk<chunk number>_PC.ome.zarr`. | ||
| The chunk number is set to `yyxx`, where yy is the resolution of the scan in micrometers, and xx is a scan number that is unique between datasets. | ||
| For example, a scan number of `402` is the second 4um scan. |
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| For example, a scan number of `402` is the second 4um scan. | |
| For example, a chunk number of `402` is the second 4um scan. |
kabilar
reviewed
Sep 20, 2024
| Datasets have the name `sub-<donor>_sample-<sample name>_chunk<chunk number>_PC.ome.zarr`. | ||
| The chunk number is set to `yyxx`, where yy is the resolution of the scan in micrometers, and xx is a scan number that is unique between datasets. | ||
| For example, a scan number of `402` is the second 4um scan. | ||
| The highest lowest resolution dataset (equivalently, highest chunk number) is the overview dataset that contains an image of the whole sample. |
There was a problem hiding this comment.
Suggested change
| The highest lowest resolution dataset (equivalently, highest chunk number) is the overview dataset that contains an image of the whole sample. | |
| The lowest resolution dataset (equivalently, highest chunk number) is the overview dataset that contains an image of the whole sample. |
kabilar
reviewed
Sep 20, 2024
kabilar
reviewed
Sep 20, 2024
| For more information on the modality see the [HiP-CT website](https://mecheng.ucl.ac.uk/hip-ct/). | ||
| Most of the time HiP-CT consists of a single 'low' (but still quite high!) resolution scan of a whole sample, and then one or more 'high' resolution scans of particular volumes of interest within the same sample. | ||
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| ## Data information |
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| ## Data information | |
| ## Data acquisition and naming |
kabilar
reviewed
Sep 20, 2024
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| Datasets have the name `sub-<donor>_sample-<sample name>_chunk<chunk number>_PC.ome.zarr`. | ||
| The chunk number is set to `yyxx`, where yy is the resolution of the scan in micrometers, and xx is a scan number that is unique between datasets. |
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This adds some docs on the HiP-CT data, including registrations, as requested by @kabilar. cc @ucbpclw