Commit 17931ecb authored by Lucy McNeill's avatar Lucy McNeill
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update README.md to reflect new crowded_foci option

parent 39fb4a8b
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......@@ -28,22 +28,22 @@ if you are looking at mouse pachytene (what synapsis is designed for), the follo
```r
SYCP3_stats <- get_pachytene(path,ecc_thresh = 0.8, area_thresh = 0.04)
foci_counts <- count_foci(path,offset_factor = 5, brush_size = 1, brush_sigma = 1, annotation = "on",WT_out = "Fancm+/+",KO_out = "Fancm-/-")
foci_counts <- count_foci(path,offset_factor = 5, brush_size = 1, brush_sigma = 1, annotation = "on",WT_out = "Fancm+/+",KO_out = "Fancm-/-", stage = "pachytene")
```
and
```r
df_dist <- measure_distances(path,offset_factor = 5, brush_size = 1, brush_sigma = 1, annotation = "on", WT_out = "Fancm+/+",KO_out = "Fancm-/-")
df_dist <- measure_distances(path,offset_factor = 5, brush_size = 1, brush_sigma = 1, annotation = "on", WT_out = "Fancm+/+",KO_out = "Fancm-/-", stage = "pachytene")
```
otherwise, for everything else, you could call something like:
```r
foci_counts <- count_foci(path,offset_factor = 5, brush_size = 1, brush_sigma = 1, annotation = "on",WT_str = "tif",WT_out ="NA",file_ext = "tif", channel2_string = "c3", channel1_string = "c2", offset_px = 0.4)
foci_counts <- count_foci(path,offset_factor = 5, brush_size = 1, brush_sigma = 1, annotation = "on",WT_str = "tif",WT_out ="NA",file_ext = "tif", channel2_string = "c3", channel1_string = "c2", offset_px = 0.4, crowded_foci = TRUE)
```
and
```r
df_dist <- measure_distances(path,offset_factor = 5, brush_size = 1, brush_sigma = 1, annotation = "on",WT_str = "tif",WT_out ="NA",file_ext = "tif", channel2_string = "c3", channel1_string = "c2", offset_px = 0.4)
df_dist <- measure_distances(path,offset_factor = 5, brush_size = 1, brush_sigma = 1, annotation = "on",WT_str = "tif",WT_out ="NA",file_ext = "tif", channel2_string = "c3", channel1_string = "c2", offset_px = 0.4, crowded_foci = TRUE)
```
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