Commit ed595247 authored by Lucy McNeill's avatar Lucy McNeill
Browse files

add auto_crop use to markdown

parent 4735bfcd
......@@ -40,7 +40,7 @@ Wayne Crismani, St Vincent's Institute of Medical Research and the University of
## Compatibility
synapsis relies heavily on the bioconductor package EBImage, which currently supports jpeg, png and tiff image files.
synapsis relies heavily on the `bioconductor` package `EBImage`, which currently supports jpeg, png and tiff image files.
Currently, synapsis also supports
......@@ -64,10 +64,19 @@ We summarise them in the following subsections:
### auto_crop
input: Original grey scale image files of (1) Synaptonemal complexes ("SC", e.g. SYCP3 anti-body) and (2) foci (e.g. MLH1, MLH3 anti-body) channels from e.g. Nikon .nd2 files.
input: Path to original grey scale image files of (1) Synaptonemal complexes ("SC", e.g. SYCP3 anti-body) (2) foci (e.g. MLH1, MLH3 anti-body) and (3) cell boundary structure (e.g. DAPI stain) channels from e.g. Nikon .nd2 files. See setup vignette for the details of getting files ready.
output: crops in SC (red) and foci (green) around individual cells.
Calling auto_crop:
```r
# using auto_crop
auto_crop_fast(path)
```
In the following figure, we show how synapsis automatically crops around a single "good" cell, starting with the original images of the two channels in Figure 1, from start to finish.
![cropping](resources/figures/cropping_procedure.png)
......
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