The Huygens File Series Tool

There are many ways in which Tiff files or other file series are named. These files can have multiple counters (referring to slices, time frames, or channels), and these counters can have arbitrary prefixes and ordering.

Hygens always supported plain Numbered Tiff series and the Leica Tiff style numbering. Huygens supports many other File-Formats as well.

Note that you only need to select the first of a properly numbered file series to load all in one go in Huygens. However, when a file is opened that appears to be part of a file series, the Huygens software shows the File Series Tool dialog. This tool automatically configures itself to load the entire series, and uses the proper dimensions. If that's what you want choose the 'load selection' and, if required, choose a smaller selection than all files. To load a single file, press the 'load single file' button in the bottom-right corner of the dialog.

The file pattern is shown in the first row in the dialog. The counters in the file name are replaced by menu buttons for selecting the appropriate dimension for each counter. The options are:

• Slice: the range of this counter becomes the z dimension.
• Time Frame: the range of this counter becomes the time dimension.
• Channel: the range of this counter becomes the channel dimension.
• Tiles: the range of this counter becomes the tile dimension and will open the Stitcher.
• Separate image: the range of this counter becomes separate images that will open separately.
• Ignore: the variable is ignored. This is useful to omit e.g. the value of time stamps.
• The value of the counter in the selected file; the value of this counter has to match the value in the selected file.

Note that the selection has to be unique, i.e. it is impossible to have ignored variables without having a Slice, Time Frame, or Channel counter.

In the second, third, and fourth row, the range for each of the counters can be defined. A range from 0 to 9 with step size 2 will load the files 0, 2, 4, 6, and 8. Note that the time (in seconds) and z sampling intervals (in nanometers) are not adapted to the step sizes.

Press the load selection button to load all files in the series into a single Huygens image. Before the dialog is closed, the tool will check if all files in the selection are really present in the directory.

Important pattern remarks

If you have a series that will have up to double or triple digits in the numbering, make sure these are followed by leading zeros. For example: image_z01.tif image_z02.tif .. image_z09.tif image_z10.tif image_z11.tif

File sorting is mostly done alphabetically and if no leading zeros are present, it will be sorted like: image_z1.tif image_z10.tif image_z11.tif image_z2.tif ... image_z9.tiff

Renaming existing file series

Renaming a series of files can take a long time if done 1 by 1. Below are some examples of utilities that you can use to rename entire image file series at once.

Ubuntu (Linux) and MacOS

For Ubuntu 18.04 and MacOS High Sierra and newer, selecting all files and pressing F2 or right-clicking and selecting 'rename' will open a mass renaming tool. This allows you to add text to the existing image filenames by using, or replace patterns with a 'find and replace text' feature.

Windows 10 and 11

On Windows there currently does not seem to be a built-in mass-renaming tool. An extension to Windows called PowerToys, created by Microsoft's own developers, allows you to enable and use the PowerRename tool. This allows you to rename multiple files with the same pattern, and even allows the use of regular expressions for more advanced users.