smartmicroscopy

Workshop Data

Inputs are shared across examples, not duplicated beside individual scripts. The current CZI files and translocation workbook live directly in this folder. Models are under DL_models/; paired training images and labels are under nucleus_data/. Add future datasets in named subdirectories and document their source, filenames, and distribution restrictions.

Treat supplied inputs as read-only. Generated tables, plots, and exports belong under the workshop’s results/ directory. CZI files at any depth are managed by Git LFS, including uppercase or mixed-case extensions. Install Git LFS before adding CZI datasets. Normal git add and git commit then use the root .gitattributes; existing history is not migrated.

After cloning, run git lfs install --local and git lfs pull from the repository root to download the datasets. GitHub LFS storage and bandwidth quotas apply. Datasets can instead be distributed separately while preserving this directory layout.

Translocation Dataset

• transloc_gfp_dapi_0_2micron.czi: CZI assay input.
• transloc_gfp_dapi_0_2micron_ngff_plate.ozx: OME-Zarr HCS archive alternative.
• plate_layout_example.xlsx: Well annotations and dose assignments. This workbook is tracked even though new .xlsx files are ignored by default; intentionally add replacement handouts with git add -f.

These inputs were copied from the local Translocation_exp dataset. Confirm permission to distribute the dataset before handing it out outside the authorized workshop audience. Analysis outputs belong in results/translocation/ at the workshop root.

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