diff --git a/_includes/ome_tiff/convert_to_ometiff_bfconvert.md b/_includes/ome_tiff/convert_to_ometiff_bfconvert.md index 72bac5b7..dcb627db 100644 --- a/_includes/ome_tiff/convert_to_ometiff_bfconvert.md +++ b/_includes/ome_tiff/convert_to_ometiff_bfconvert.md @@ -4,12 +4,15 @@ 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. @@ -17,40 +20,26 @@ 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: