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Notebook for microscopy course project 1 #2

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tzulueta
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Created a notebook to investigate the effects of DMSO in nuclear morphology. Some caveats/issues:

  • we don't have the size of the z step used during acquisition so we cannot do a proper 3D analysis
  • I computed the mean 2D metrics for each z plane and then the means for all the z planes per embryo. We could take different approaches for this (i.e. compute the mean for all the nuclei of the embryo at once)
  • I computed the results for a few z-slices per embryo as it was taking a long time. We may want to think how to deal with this problem

AybukeKY
AybukeKY approved these changes Feb 25, 2025
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LGTM. Can we use GPUs on google colab to make it faster? Or we can ask for VMs. And leave the parallelisation as a group task. I think J-M mentioned they have a notebook that does parallelisation on cellpose.

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@tzulueta @AybukeKY