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Co-authored-by: Kabilar Gunalan <[email protected]>
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dstansby and kabilar authored Sep 30, 2024
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Expand Up @@ -4,16 +4,16 @@ HiP-CT stands for hierarchical phase-contrast tomography.
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.

## Data information
## Data acquisition and naming

There are HiP-CT scans of two donors, S45 and I58.
The data are part of the [Pilot human brains dataset](https://lincbrain.org/dandiset/000005) on lincbrain.

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 are then one or more datsets at higher resolution.
For example, a chunk number of `402` is the second 4um scan.
The 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 datasets at higher resolution.

## Registration

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