The bfconvert command line tool can be used to convert files between supported formats.
bfconvert with no options displays a summary of available options.
To convert a file to single output file (e.g. TIFF):
bfconvert /path/to/input output.tiff
The output file format is determined by the extension of the output file, e.g. .tiff for TIFF files, .ome.tiff for OME-TIFF, .png for PNG.
Passes options expressed as key/value pairs:
bfconvert -option key value /path/to/input /path/to/output
e.g. additional writer options, see Additional reader and writer options:
bfconvert -option ometiff.companion converted.companion.ome input.fake converted.ome.tiff
New in version 5.4.0.
All images in the input file are converted by default. To convert only one series:
bfconvert -series 0 /path/to/input output-first-series.tiff
To convert only one timepoint:
bfconvert -timepoint 0 /path/to/input output-first-timepoint.tiff
To convert only one channel:
bfconvert -channel 0 /path/to/input output-first-channel.tiff
To convert only one Z section:
bfconvert -z 0 /path/to/input output-first-z.tiff
To convert images between certain indices (inclusive):
bfconvert -range 0 2 /path/to/input output-first-3-images.tiff
All images larger than 4096×4096 will be saved as a set of tiles if the output format supports doing so. The default tile size is determined by the input format, and can be overridden like this:
bfconvert -tilex 512 -tiley 512 /path/to/input output-512x512-tiles.tiff
-tilex is the width in pixels of each tile; -tiley is the height in pixels of each tile. The last row and column of tiles may be slightly smaller if the image width and height are not multiples of the specified tile width and height. Note that specifying -tilex and -tiley will cause tiles to be written even if the image is smaller than 4096×4096.
Also note that the specified tile size will affect performance. If large amounts of data are being processed, it is a good idea to try converting a single tile with a few different tile sizes using the -crop option. This gives an idea of what the most performant size will be.
For very large images, it may also be useful to convert a small tile from the image instead of reading everything into memory. To convert the upper-left-most 512×512 tile from the images:
bfconvert -crop 0,0,512,512 /path/to/file output-512x512-crop.tiff
The parameter to -crop is of the format x,y,width,height. The (x, y) coordinate (0, 0) is the upper-left corner of the image; x + width must be less than or equal to the image width and y + height must be less than or equal to the image height.
Images can also be written to multiple files by specifying a pattern string in the output file. For example, to write one series, timepoint, channel, and Z section per file:
bfconvert /path/to/input output_series_%s_Z%z_C%c_T%t.tiff
%s is the series index, %z is the Z section index, %c is the channel index, and %t is the timepoint index (all indices begin at 0).
For large images in particular, it can also be useful to write each tile to a separate file:
bfconvert -tilex 512 -tiley 512 /path/to/input output_tile_%x_%y_%m.jpg
%x is the row index of the tile, %y is the column index of the tile, and %m is the overall tile index. As above, all indices begin at 0. Note that if %x or %y is included in the file name pattern, then the other must be included too. The only exception is if %m was also included in the pattern.
By default, all images will be written uncompressed. Supported compression modes vary based upon the output format, but when multiple modes are available the compression can be changed using the -compression option. For example, to use LZW compression in a TIFF file:
bfconvert -compression LZW /path/to/input output-lzw.tiff
If the specified output file already exists, bfconvert will prompt to overwrite the file. When running bfconvert non-interactively, it may be useful to always allow bfconvert to overwrite the output file:
bfconvert -overwrite /path/to/input /path/to/output
To always exit without overwriting:
bfconvert -nooverwrite /path/to/input /path/to/output
To disable the conversion of lookup tables, leaving the output file without any lookup tables:
bfconvert -nolookup /path/to/input /path/to/output
New in version 5.2.1.
This option forces the writing of a BigTiff file:
bfconvert -bigtiff /path/to/input output.ome.tiff
New in version 5.1.2.
The -bigtiff option is not necessary if a BigTiff extension is used for the output file, e.g.:
bfconvert /path/to/input output.ome.btf
This option is used alongside a pattern string when writing an image to multiple files. When set this will enforce zero padding on the filename indexes set in the provided pattern string:
bfconvert /path/to/input output_xy%sz%zc%ct%t.ome.tif -padded
New in version 5.2.2.