implement report templates

[danilexn]

Feature Description

For the different steps of the openst pipeline, implement report templates (HTML), as we have for the alignment.

Use Case

This helps to diagnose whether the individual steps ran properly; similar to spacemake QC reports and automated analysis.

Proposed Implementation

Follow the current standard of the report template used for the pairwise alignment.

We would like to implement this for:

• Extraction of barcode coordinates (how many over the total have coordinates, how the tiles look like).
• Complete the pairwise alignment to account for the fiducial frame detection
• For the manual alignment (with GUI), showing the keypoints. We can recycle most of the code for the pairwise alignment report template.
• Segmentation metadata & results (show images, but also summary statistics on cell density, number of cells, average size, etc).
• Assign transcripts to (segmented) cells
• Stitching of spatial data
• Stitching of images (get from ImageJ metadata)
• 3D reconstruction (generate reports from STIM results, show low-res renderings in 3D using ipyvolume?)

Optionally

• We can use the python version of the spacemake automated analysis to create similar reports, but after segmentation.

Additional Information

Comment below if any other reports would be necessary.