updates to ome_tiff

_includes/ome_tiff/convert_to_ometiff_bfconvert.md

@@ -4,53 +4,42 @@ and it uses Fiji to inspect the content of the OME-TIFF data.
 Note that bfconvert is capable of generating a variety of other formats (in addition to OME-TIFF)
 such as tiff, png, jpeg, OME-XML, etc., although we will focus on the OME-TIFF in this activity.
 
+Before starting, make sure you have downloaded the `xyz__multiple_images.czi` somewhere convenient.
+We refer to this input path as `/path/to/xyz__multiple_images.czi`. 
+Also create an output folder for OME-TIFF. We refer to this output folder as `/path/to/OME-TIFFs`
+
+
 **Basic conversion**
 
 ```bash 
-bfconvert \
-~/ome_zarr_course/data/czi/xyz__multiple_images.czi \
-~/ome_zarr_course/data/OME-TIFF/xyz__multiple_images.ome.tiff
+bfconvert /path/to/xyz__multiple_images.czi /path/to/OME-TIFFs/xyz__multiple_images.ome.tiff
 ```
 This will create an OME-TIFF containing two images. Often, this is not convenient, and we would
 prefer to specify a single series for conversion.
 
 **Select one series and convert**
 
 ```bash
-bfconvert \
--series 1 \
-~/ome_zarr_course/data/czi/xyz__multiple_images.czi \
-~/ome_zarr_course/data/OME-TIFF/xyz__multiple_images_s1.ome.tiff
+bfconvert -series 1 /path/to/xyz__multiple_images.czi /path/to/OME-TIFFs/xyz__multiple_images_s1.ome.tiff
 ```
 
 **Specify compression**
 ```bash
-bfconvert \
--series 1 \
--compression "JPEG-2000 Lossy" \
-~/ome_zarr_course/data/czi/xyz__multiple_images.czi \
-~/ome_zarr_course/data/OME-TIFF/xyz__multiple_images_s1_compressed.ome.tiff
+bfconvert -series 1 -compression "JPEG-2000 Lossy" /path/to/xyz__multiple_images.czi /path/to/OME-TIFFs/xyz__multiple_images_s1_compressed.ome.tiff
 ```
 **Check output size**
 ```bash
-du -sh ~/ome_zarr_course/data/OME-TIFF/*
+du -sh /path/to/OME-TIFFs/* # unix
 ```
-**Select one series and specify z-range**
+**Select one series and specify z-range** \
+Use the option `-range START END`
 ```bash 
-bfconvert \
--series 0 \
- -range 0 0 \
-~/ome_zarr_course/data/czi/xyz__multiple_images.czi \
-~/ome_zarr_course/data/OME-TIFF/xyz__multiple_images_s0_range0-1.ome.tiff
+bfconvert -series 0 -range 0 0 /path/to/xyz__multiple_images.czi /path/to/OME-TIFFs/xyz__multiple_images_s0_range0-0.ome.tiff
 ```
-**Crop in 3-D**
+**Crop in 3-D** \
+Use the option `-crop x,y,WIDTH,HEIGHT`
 ```bash 
-bfconvert \
--series 0 \
--range 0 0 \
--crop 20,30,100,100 \
-~/ome_zarr_course/data/czi/xyz__multiple_images.czi \
-~/ome_zarr_course/data/OME-TIFF/xyz__multiple_images_s0_crop3D.ome.tiff
+bfconvert -series 0 -range 0 0 -crop 20,30,100,100 /path/to/xyz__multiple_images.czi /path/to/OME-TIFFs/xyz__multiple_images_s0_crop3D.ome.tiff
 ```
 
 Inspect the output OME-TIFFs using Fiji: