SVI-wiki: Huygens Command

Save an image to disk

Relevant information

Supported File Formats
ICSfile Format

Tcl-Huygens reference

img save <filename>

Supported file formats

hdf5: Hierarchical Data Format
ics: Image Cytometry Standard (ICS) format.
ics2: Image Cytometry Standard (ICS) format, version 2.0. ICS 2.0 is an extension to the ICS-standard. It combines the header information and the raw data into a single 'ics-file'. Reading and writing ics2 type files is implemented starting from Huygens 2.4. The ics2 format is not yet fully developed. It is given here for the sake of completeness and is only accessible using -type ics2 save option.
imaris: Bitplane A.G. Imaris Classic format.
ppm: stores the first three channels of a 2D image in ppm format. Images with higher dimensionality are not supported.
OME: The Open Microscopy Environment (OME-XML) format
pic: Bio-Rad Confocal format.
r3d: The Delta Vision IMSubs format.
jpeg: JPEG format. Supported in Huygens Core only. Saves single channel images in gray scale and two or three channel images in RGB. Channel four and up are ignored. The quality level can be set from 0 to 100 percent using the -q option.
tiff, tiff16: If the image is 2D, or -tiffMultiDir was specified, a single channel image will be exported to a single tiff file. If -tiffMultiDir was specified multi-channel images will be exported to a RGB 8bit single tif file. Otherwise, the data will be exported to a suffixed series of single channel 8- or 16-bit TIFF files. A 29 plane time series of 10 frames with base name `Series08' will be saved as:
Series08_t00_z000.tif Series08_t00_z001.tif ... Series08_t01_z000.tif Series08_t01_z001.tif ... Series08_t09_z027.tif Series08_t09_z028.tif
For TIFF file formats, the option -cmode determines how the intensities are adapted in case a data type conversion is necessary:
- stretch: The intensity range between zero and the maximum is stretched to keep the contrast. (If some negative intensity is in the image, it is clipped). This happens separately per channel. Use this mode for visualization purposes. This is the default option in silent mode.
- scale: The non-negative intensities in the different channels are scaled proportionally (linked). The ratios between their intensities are preserved. The scaling factor is reported. Use this mode if further analysis is necessary.
- clip: the numeric values are written directly to the destination without scaling. If the values are larger than the destination possible maximum, they are clipped. Use this mode carefully, taking care in your scripts of necessary preliminar conversions to avoid data losses.
- query: In interative (non-silent) mode the user will be prompted to select one of the above.
Even when a data conversion is not necessary (when a signed Integer Type image is saved to a unsigned 16 bit TIFF file) the -cmode option will control whether the data is multiplied by 2 to make use of the extra available bit (stretch) or written directly (clip). In any case only the positive values are saved. See Tiff Scaling for more details.
tiffrgb: the first 3 channels of a 2D-4D image in a series of RGB Tiff files . The numbering scheme is as follows:
- 2D image: the image is saved without a numbering scheme.
- 3D image: the numbering will be simple like: foo000.tif .. foo031.tif.
- 4D image: the scheme outlined above is adopted.
The following cases will be saved as a single file:
- 2D single and multi channel.
- 3D single channel (XYZ, XYT).
In the following cases the image will be saved as a file series:
- Multi channel stacks (XYZ) and multi channel 2D time series (XYT) will be exported to a series of files, in which every file holds the data of a single image. The files are denoted as : name01, name02 ...
- 4D images (XYZT) will be exported to a series in which every file holds the data of a single stack. The series will look like: name00101, name00201,..., name00102, name 00202, ... in which the first three digits are the time point, and the last two are the channel number.
Please note that only three channels are imported and exported in this format.

Returns: path to the written file.

Note: .ics or .ids suffixes are stripped.

Do not confound with...

hu_saveDef

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