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View Code? Open in Web Editor NEWA microscopy image processing toolkit.
A microscopy image processing toolkit.
For some reason image flipping no longer works as expected. This might be because we are using slicing in a potentially undefined way.
Because of this line stitching consumes a lot of memory.
We should find a way to not read the entire array into memory at once when calling persist.
Right now the entire Reader class will output unhelpful stack traces or even worse: will fail in a later part of the pipeline. We should output helpful messages instead to help users diagnose problems and fail fast by checking user inputs.
Right now reader arguments get passed in when the pipeline gets called rather than when the pipeline gets created see here.
We should make this consistent with other components instead.
ome.tiff files don't always have channel names e.g. if the user has saved a file with only one channel. We should check for this here
Right now bead finding assumes that beads are high-intensity circles. But this isn't always the case: e.g. when imaging in brightfield or when things are bound to the surface of the bead.
We should make it so both types of bead can be found. Ideally this would happen automatically without the user needing to specify a bead finding method.
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