Tagged image file format (TIFF)
Tagged Image File Format (abbreviated TIFF) is a widely used file format for storing images. It is flexible and adaptable, and can handle multiple images and metadata in a single file through the inclusion of "tags" in the file header. Tags can indicate the basic geometry of the image, such as its size, or define how the image data is arranged and whether various image compression options are used.
Unfortunately, there are many non-standard TIFF variants and they are nearly always too limited in saving specific microscopy metadata. Better alternatives are therefore the more standardized formats like HDF5, OME-Tiff, or ICS. More on file formats.
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Open TIFF files in Huygens
The Huygens Software can read TIFF files by default, including the most popular non-standard variants created by microscope manufactures. This includes file formats like the Olympus Fluoview TIFF format (.oif) and the OME-TIFF file format. For a detailed overview of all TIFF file variants the Huygens software can read, see all supported File Formats.3D, time series and multi-channel files
Within Huygens it is possible to open 3D, time series and multi-channel TIFF file series in multiple ways. When opening a file manually, the Huygens File Series Tool is automatically used. It is also possible to load file series with the Huygens Workflow Processor, which allow batch processing of TIFF file series. Huygens detects many types of file series, however, in some cases renaming to for example the Leica Tiff style numbering may be required to open file series.When opening a TIFF file, Huygens will automatically scan the directory for files with a matching name to identify series. In case Huygens recognizes the file is part of a series, it will automatically open the file series tool. Within the file series tool, you can edit which files should be loaded. The tool will automatically configures itself to load the entire series from the selected file onward, and uses the proper dimensions. The counters in the file name are replaced by menu buttons for adjusting the automatic dimension for each counter if needed. The options are:
- Slice: Becomes the z dimension.
- Time Frame: Becomes the time dimension.
- Channel: Becomes the channel dimension.
- Tiles: Becomes the tile dimension and will open the Stitcher.
- Ignore: The variable is ignored.
- The value of the counter: Only select specific value for counter.
File Series Tool
The Huygens File Series Tool. Adjust how a TIFF file serie should be loaded into Huygens
With the Huygens Workflow processor, you can also open tiff file series to use them within your workflow pipeline. To open TIFF file series within a pipeline of the workflow processor, use the Load img. series task in your workflow. Like the Huygens File Series Tool, you need to edit and verify how Huygens should load the file series. Note that for each workflow one file series can loaded. For processing multiple file series quickly with the Workflow Processor, a template for the workflow can be used.
Workflow Processor
Loading File Series in the Huygens Workflow Processor
Save TIFF files in Huygens
Within Huygens it is possible to save images in the TIFF file format. You can save as unsigned integer 8 bit, 16 bit or 3x8 bit RGB. We however highly recommend using another file format that is well-supported, preserves the metadata properly, and keeps the information about image dimensions. It is therefore best to save your valuable image data as ICS2 or HDF5.Scaling
The TIFF export File Formats available in the Huygens Software may require that the data is rescaled to make the intensities fit the destination format's Dynamic Range. If not rescaled, data clipping or a loss of dynamic range (intensity resolution) may occur. If you are interested in quantifying your data, you may want to pay attention to the scaling of images and how to treat them properly (see also Signal Quantification). In case the current range of the image data does not fit in the range of the selected TIFF type, the following choices to reduce the range are offered:- Contrast stretch (positive data range for each channel is adapted to the TIFF range, the different per-channel factors are not reported)
- Linked scale (as stretch, but now the relation between channels is retained: the same factor is applied to all channels that stretches the one with maximum intensity to the TIFF range. The factor is reported by Huygens Task reports.)
- Clip (positive data outside the TIFF range is clipped to that range)
Note that for a single channel image, the first two modes are equivalent, but only with linked scale the scaling factor is reported in the Task reports. Furthermore, all negative integers are always clipped for all rescaling options. To prevent clipping of negative integers, make sure that you convert your image to unsigned integer before saving.
3D, time series and multi-channel files
It is possible to save 3D, time series and multi-channel files as a series of TIFF files. A TIFF file can contain a single image or several ones, which is called a multi-directory TIFF. This is useful to store a whole 3D stack in a single file. When saving a 3D image as a TIFF file in Huygens, the option is given to save the z-stack either as a single file or as one file per slice. For time series and multi-channel images, Huygens creates always a separate file for each time frame and channel respectively. The Huygens Software writes TIFF series with the Leica style numbering if there are multiple channels, slices or frames. Example numbering: ImageName_t01_z001_ch01.tif.
Options for saving a 3D multi-channel image as TIFF
TIFF File conversion
The Huygens Software can be used perfectly to convert TIFF files to other supported image formats. There are several ways to succesfully convert your TIFF file to another format within Huygens. It can be done manually using the tools in Huygens, or automatically with the Huygens Workflow Processor.The easiest way to convert a TIFF file with the Huygens Software is by opening the image and save it in another file format, like ICS. For a full list of all file formats the Huygens Software can save, see File Formats. Before saving your image you can use the Tools in Huygens if needed to correct or adjust the image. With the Tools you can split channels, crop the image or convert dimensions in case the dimensions are not read correctly. In Huygens Professional you can also use the Operations Window to correct or adjust the image.
The Tools menu in Huygens Essential.
With the Huygens Workflow processor, you can also automatically convert TIFF files into another file format with a workflow pipeline. This workflow will automatically open images from a selected folder, and save them in a chosen file format into a set save location. Use the Select image(s) task to select the folder where the TIFF images stored. As second task use the Set save location task to select the file format in which the TIFF files should be converted to and the location where the images should be saved. You can save the file conversion workflow as a template for more frequent use. Running this workflow will automatically convert all files in a folder to the chosen file format.
Workflow Processor
Automatic file conversion workflow in the Huygens Workflow Processor