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wiki: add images/videos #4

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2 of 8 tasks
danilexn opened this issue Oct 20, 2023 · 0 comments
Open
2 of 8 tasks

wiki: add images/videos #4

danilexn opened this issue Oct 20, 2023 · 0 comments
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documentation Improvements or additions to documentation

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@danilexn
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danilexn commented Oct 20, 2023

Issue/Improvement Description

We need to add images and videos for illustrating several sections - especially, computational step-by-step guide.

Context

I would like to have graphical summaries (like the ones in the paper, or some new ones for the website), to illustrate the steps - only text is a bit dry. Not only images, but we can also put interactive visualizations, ie experimental/capture_area_generation/#breaking-the-flow-cells-into-capture-areas

Proposed Changes

  • computational/preprocessing_sequencing/#flow-cell-related-terms: needs an illustration of the flow cell
  • computational/preprocessing_sequencing/#global-spatial-coordinates-tile-stitching: needs an illustration of what the 'global' stitching means
  • computational/preprocessing_imaging: needs images for an example tissue before tile stitching and after tile stitching (illustration); also, an example before and after image preprocessing (e.g., with CUT, for correcting the irregularities in focus)
  • computational/pairwise_alignment: needs an outline of how the alignment works (maybe the figure from the paper?)
  • computational/pairwise_alignment/#required-input-data: requires images of the fiducial features at high and low resolution, to illustrate what is a good-enough resolution.
  • computational/pairwise_alignment/#manual-workflow: include some pictures of the GUI here, and make the video tutorial
  • computational/generate_expression_matrix: include some example of the cell segmentation, and a graphical summary of what we mean with assigning transcripts to the mask.
  • computational/threed_reconstruction: add images of the 3d, and potentially a browseable 3d volume.

Additional Information

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@danilexn danilexn added the documentation Improvements or additions to documentation label Oct 20, 2023
@danilexn danilexn self-assigned this Oct 20, 2023
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