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Merge pull request #41 from rajewsky-lab/danilexn-patch-1
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Daniel León Periñán authored Apr 16, 2024
2 parents e8239ac + 7771d7e commit cc54997
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6 changes: 3 additions & 3 deletions docs/computational/pairwise_alignment.md
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Expand Up @@ -32,13 +32,13 @@ Other formats, i.e., `jpeg` and `png` are also compatible. Make sure that the im
and not a downsampled version. As a rule of thumb, at least a few fiducial markers must be clearly distinguishable.

=== "Good visibility"
![Good visibility](../static/img/compu_pairwise_align_fiducial_visibility/good_visibility.webp){ loading=lazy }
![Good visibility](../../static/img/compu_pairwise_align_fiducial_visibility/good_visibility.webp){ loading=lazy }

=== "_Fair_ visibility"
![Fair visibility](../static/img/compu_pairwise_align_fiducial_visibility/fair_visibility.webp){ loading=lazy }
![Fair visibility](../../static/img/compu_pairwise_align_fiducial_visibility/fair_visibility.webp){ loading=lazy }

=== "_Poor_ visibility"
![Poor visibility](../static/img/compu_pairwise_align_fiducial_visibility/poor_visibility.webp){ loading=lazy }
![Poor visibility](../../static/img/compu_pairwise_align_fiducial_visibility/poor_visibility.webp){ loading=lazy }

### Spatial transcriptomics modality
The expected input for the spatial transcriptomics modality is a single [h5ad] file containing all
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2 changes: 1 addition & 1 deletion docs/computational/preprocessing_imaging.md
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# Preprocessing of imaging data
If you used our same experimental setup for imaging, you will obtain individual images
as a result of performing imaging of the stained tissue in a tile-scan fashion. From this point,
the open=ST pipeline expects to have a single image for the whole tile-scan, rather than individual files
the Open-ST pipeline expects to have a single image for the whole tile-scan, rather than individual files
per tile.

This step depends on the microscope used for imaging. In [our implementation](../experimental/library_preparation.md#he-staining-and-imaging), we used a
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