This application takes a TIFF file and converts it into Priism's native file format. With the Convert menu select whether you are converting a single file or are combining a series of TIFF files into one Priism file. For a single file, enter the name in TIFF File field; combining multiple files is described below. Enter the destination file or window in the MRC File field and press DoIt to perform the conversion.
Overview | File Selection | Multiple Image TIFFs | Multiple Files | Palettes | Messages
Priism | Categories | Applications
The converter either does one file at a time (the Single File option in the Convert menu) or combines a numbered series of files (the Numbered Series option). The inputs not relevant to the option selected will be grayed out.
Overview | File Selection | Multiple Image TIFFs | Multiple Files | Palettes | Messages
When converting a single TIFF file, you have the option of setting how to handle the case when multiple images are present in the file. The default is to only read the first image in the file. The other options are to treat the images as z-sections, separate time measurements, or wavelengths. Treating multiple images as waves does not work when each image has multiple wavelengths already (i.e. RGB data or when converting files with color tables to RGB).
When working converting a series of TIFF files, only the first image in each is read.
Overview | File Selection | Multiple Image Tiffs | Multiple Files | Palettes | Messages
The Numbered Series option in the Convert menu allows you to combine multiple TIFF files into one Priism dataset. The files must follow a special naming convention. The strings in the Directory and Prefix fields give the first part of each file name. For instance, if /scratch/exp1 is the directory and the prefix is movie1, then all the file names must start with /scratch/exp1/movie1.
The remaining portion of each file name is determined by the Z Start/# and T Start/#. The second integer in each of these fields (let's call them z1 and t1) specifies the number of sections in that dimension; for each section there must be a TIFF file. So z1 times t1 TIFF files will be needed in total. In each of these file names the z section and t section is encoded. The z section is included in the file as _z# where # is the z section number plus the first integer in Z Start/# written as a decimal. The number of decimal places in the number is set by the largest number; smaller numbers are padded on the left with zeroes. The t section is included in a similar fashion.
So the whole file name appears as Directory/Prefix_z#_t#.tif. There are a handful of special cases. If t1 is not greater than 1, then the _t# part is omitted and the _z# portion is included without the _z. If z1 is not greater than 1, then the _z# part is omitted.
Overview | File Selection | Multiple Image TIFFs | Multiple Files | Palettes | Messages
For pseudocolor TIFF files, which have a color table (palette) that maps the image values to full color RGB, the conversion can use the color table and create an output file with three waves (the as RGB option), or the color table can be ignored and the raw image values will be stored in a single wave (the as Grayscale or as Inverted Grayscale options). The former gives better results when the image in the TIFF file was derived from a full color image. The latter is better if you are interested in data values from an originally single color image which has had a color table applied for visualization purposes.
For images without a color table (full-color RGB or grayscales), this setting has no effect. When an image with a color table is converted, messages to that effect will be written in the log.
Overview | File Selection | Multiple Image TIFFs | Multiple Files | Palettes | Messages
Errors that cause the conversion to fail will cause a dialog to appear telling generally in what stage of the process the error occurred. For more information about why the conversion failed or possible non-fatal problems with the conversion, the View Log button in the dialog can be used to display the messages generated. Messages that start with tiff2mrc are generated by the application itself; other messages are from the underlying conversion library.
Overview | File Selection | Multiple Image TIFFs | Multiple Files | Palettes | Messages