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Address several pieces of #3 in
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 the vignette
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Nick-Eagles committed Jul 26, 2024
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8 changes: 5 additions & 3 deletions vignettes/visiumStitched.Rmd
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Expand Up @@ -144,7 +144,7 @@ sample_info$spaceranger_dir <- file.path(
sample_info
```

# Preparing Images for Fiji
# Preparing Inputs to Fiji

The `visiumStitched` workflow makes use of [Fiji](https://imagej.net/software/fiji/), a
distribution of the `ImageJ` image-processing software, which includes an interface for
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# Building a `SpatialExperiment`

## Stitching Images with Fiji

Before building a `SpatialExperiment` for a stitched dataset, we must align the images for each
group in Fiji. Check out [this video](https://www.youtube.com/watch?v=kFLtpK3qbSY) for a
guide through this process with the example data.

<iframe width="560" height="315" src="https://www.youtube.com/embed/kFLtpK3qbSY?si=CF-rv7Nd5yc7W6nC" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" referrerpolicy="strict-origin-when-cross-origin" allowfullscreen></iframe>

## Parsing Outputs from Fiji
## Creating Group-Level Samples

From the Fiji alignment, two output files will be produced: an `XML` file specifying rigid
affine transformations for each
Expand Down Expand Up @@ -296,7 +298,7 @@ variation across spots can bias the apparent distribution. Later, we'll show tha
normalization is critical to producing a visually seamless transition between overlapping
capture areas.

## Array coordinates
## Defining Array Coordinates

Given that the stitched data is larger than a default Visium capture area, `add_array_coords()` (which is used internally by `build_spe()`) recomputed the array coordinates (i.e. `spe$array_row` and `spe$array_col`) to more sensibly index the stitched data.

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