The Liberali's often have setups where the metadata (specifically the .mrf file) contains channels that were then not acquired. The way this comes up is if a user adds more channels in the microscopy software, but then never uses them.
This becomes and issue when that additional channel has different dimensions. For example, the additional channel is brightfield and has a lower resolution. In that case, we get an error like this one:
In practice, there are no consistency issues in the acquired images, only in the channel metadata.
2 areas for improvement:
a) improve the error message
b) handle this more flexibly: Maybe we can pre-filter the channels and only check channels that were imaged / channels provided as allowed channels
Here are example metadata files that reproduce this issue. They need to be renamed to .mlf & .mrf to work with the parsing again. I'll need to see if I find time soon to take a closer look
The Liberali's often have setups where the metadata (specifically the .mrf file) contains channels that were then not acquired. The way this comes up is if a user adds more channels in the microscopy software, but then never uses them. This becomes and issue when that additional channel has different dimensions. For example, the additional channel is brightfield and has a lower resolution. In that case, we get an error like this one:
In practice, there are no consistency issues in the acquired images, only in the channel metadata.
2 areas for improvement: a) improve the error message b) handle this more flexibly: Maybe we can pre-filter the channels and only check channels that were imaged / channels provided as allowed channels