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hoogenboom-group / scripted-render-pipeline

automated pipeline interfacing with render-ws rest api
GNU General Public License v3.0
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Intensity clipping when converting to webknossos.wkw format goes wrong #28

Open arentkievits opened 1 month ago

arentkievits commented 1 month ago

Datasets processed with exporter have weird histograms in WebKnossos. In the high intensity range, biological features are clipped, which should only be minimal. This is problematic.

Example of a weird histogram: image

Example of a normal histogram: image

thopp-tudelft commented 1 month ago

the top dataset has a very high amount of artifacts, this definitely causes the clipping to go wrong, in order to preserve depth in the biology of the sample a higher lower bound for the percentile parameter in the import to render needs to be selected, eg 30-99 percentile clipping. alternatively we can revise our import code to find and ignore such artifacts through some sort of masking. the export code does not calculate the clipping, this is done on import.