Image Processing

ome-tiff to zarr conversion

The data acquired by Micromanager is converted to ome zarr format using iohub library.

Quantitative label-free (phase) reconstruction

Brightfield volumes were reconstructed to get phase information using waveorder. Phase image is more informative as it enhances the morphological features visible in the brightfield images and adds information on the relative density distribution in cells.

Image registration

The three image channels were registered using biahub. BF and fluorescence channels were misregistered due to different views of the two different cameras, and the two fluorescence channels were misregistered due to differences in optics used for filtering the specific wavelengths of light.

Image download and visualization

Download the complete high-resolution dataset with multiple field-of-views for all displayed conditions using following command:

wget -m -np -nH --cut-dirs=3 -R "index.html*"https://public.czbiohub.org/organelle_box/datasets/A549/organelle_box_v1.zarr"

800 x 800 pixel crop of one field-of-view is displayed.

You can visualize the zarr data using napari.

See napari-iohub and napari-ome-zarr for napari plugins to interact with OME Zarr data.