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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
None
The text was updated successfully, but these errors were encountered:
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 cellcomputational/preprocessing_sequencing/#global-spatial-coordinates-tile-stitching
: needs an illustration of what the 'global' stitching meanscomputational/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 tutorialcomputational/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
None
The text was updated successfully, but these errors were encountered: