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sciai-lab / batchlib

Batch procesing for high-throughput screening data
MIT License
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Cell tables: add cell anchor #128

Closed tischi closed 4 years ago

tischi commented 4 years ago

@constantinpape Since we are also now looking at single cell stuff, I think it would be very useful to have anchor_x and anchor_y coordinates in the cell tables (both in the hdf5 and the excel tables). Would that be possible to add?

constantinpape commented 4 years ago

Sure, no problem. Will add it in the next run.

constantinpape commented 4 years ago

@tischi this is pretty easy to implement. In the h5 tables, I will just have another table for the cell segmentation called properties which contains cell sizes, anchors and could be extended with other, intensity independent, attributes.

Would you also want this to be exported to the excel tables I produce for you? In there, I would probably not export an extra table, but just add it to the cell tables that are already exported. What do you think?

tischi commented 4 years ago

In the h5 tables, I will just have another table for the cell segmentation called properties which contains cell sizes, anchors and could be extended with other, intensity independent, attributes.

makes sense

Would you also want this to be exported to the excel tables I produce for you? In there, I would probably not export an extra table, but just add it to the cell tables that are already exported. What do you think?

Just one table is much easier for me. In fact, also in the hdf5 just having one table would be more convenient, I think.

constantinpape commented 4 years ago

Just one table is much easier for me. In fact, also in the hdf5 just having one table would be more convenient, I think.

In the hdf5 that is not a good idea due to the way we compute these things; this should all stay modular!

For the export, no problem.

constantinpape commented 4 years ago

Implemented in #130, but I still need to add it to the excel tables, will do tomorrow.

constantinpape commented 4 years ago

@tischi this is all implemented now; the new excel cell tables will have columns anchor_x and anchor_y.