Convert to Priism's Native Format from TIFF

Overview

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. The application also has a command line interface if that is more convenient for you.

Topics

Overview | File Selection | Multiple Image TIFFs | Multiple Files | Palettes | Messages | Command Line

Related Priism Topics

Priism

File Selection

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.

Topics

Overview | File Selection | Multiple Image TIFFs | Multiple Files | Palettes | Messages | Command Line

TIFF Files With Multiple Images

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.

Topics

Overview | File Selection | Multiple Image Tiffs | Multiple Files | Palettes | Messages | Command Line

Combining Multiple Files

The Numbered Series option in the Convert menu allows you to combine multiple TIFF files into one Priism dataset. To select the form of the input file names use the "Name format" menu. That menu has three options for predefined file name formats and a fourth that allows for a custom format. For all of the predefined formats, the file names will start with the contents of the "Directory" field, followed by a slash, followed by the contents of the "Prefix" field. The remainder of the file name depends on which predefined format you select:

prefix_z#_t#.tif

After the prefix, the file name will have _z appended followed by the z section number written out, in decimal, with as many digits as needed for the largest z section number (if the section number has fewer digits than the largest z section number, leading zeros will be inserted). That will be followed by _t and then the time point number written out, in decimal, with as many digits as needed for the largest time point number (if the time point number has fewer digits than the largest time point number, leading zeros will be inserted). The file name will end with a .tif extension. This option is equivalent to using the custom file name template, %d/%p_z%az_t%at.tif.

prefix_z#.tif

After the prefix, the file name will have _z appended followed by the z section number written out, in decimal, with as many digits as needed for the largest z section number (if the section number has fewer digits than the largest z section number, leading zeros will be inserted). The file name will end with a .tif extension. This option is equivalent to using the custom file name template, %d/%p_z%az.tif.

prefix_t#.tif

After the prefix, the file name will have _t appended followed by the time point number written out, in decimal, with as many digits as needed for the largest time point number (if the time point number has fewer digits than the largest time point number, leading zeros will be inserted). The file name will end with a .tif extension. This option is equivalent to using the custom file name template, %d/%p_t%at.tif.

If you select the "custom template" option from the "Name format" menu, the input file names will be generated from the contents of the "Template" field. When generating file names, special conversion codes are expanded in the template. The conversion codes have the following general form: %[width]code. The recognized codes are:

%

Causes a percent sign to be inserted in the file name.

d

This conversion code is replaced with the contents of the "Directory" field.

p

This conversion code is replaced with the contents of the "Prefix" field.

z

This conversion code is replaced with the z section number.

t

This conversion code is replaced with the time point number.

width is optional and may be used with the z and t codes to specify the minimum number of digits which are used to display the index value. width may be a positive integer indicating the minimum number of digits to use or the letter a to indicate that the minimum number of digits should be the number of digits in the maximum corresponding index. If an index would have less than the minimum number of digits, leading zeros are added to fill in the missing portion.

As an example of a custom template, if you wanted to combine f0001.tif through f1000.tif from the directory /var/tmp as time points in a single MRC file. You would select "custom template" from the "Name format" menu, enter /var/tmp in the "Directory" field, make sure the "Prefix" field was empty, enter %d/f%4t.tif in the "Template" field, set the range of z indices to start at zero and end at zero with a step of one, and set the range of time points to start at one and end at one thousand with a step of one.

The "Z Start/End/Step" and "T Start/End/Step" fields set the range of z and time point indices, respectively, to use when generating file names. The first value in each field is the starting value, s, to use; the second value is the last possible value, e, to use; and the third value is the increment, i. The indices used will be s, s + i, ..., s + n * i. If i is greater than zero, n is the largest integer such that s + n * i is less than or equal to e. If i is less than zero, n is the largest integer such that s + n * i is greater than or equal to e. s and e must be greater than or equal to zero. i must not be equal to zero.

Topics

Overview | File Selection | Multiple Image TIFFs | Multiple Files | Palettes | Messages | Command Line

Palettes

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.

Topics

Overview | File Selection | Multiple Image TIFFs | Multiple Files | Palettes | Messages | Command Line

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.

Topics

Overview | File Selection | Multiple Image TIFFs | Multiple Files | Palettes | Messages | Command Line

Command Line

The command line syntax for tiff2mrc is
tiff2mrc options output_file_name

options may be one or more of the following; you must specify either the -in or -template options to indicate which input file or files to use.

-dir=dir

Sets the name of the directory to use in the input file name template. The -in or -template options control whether or not a file name template is used to generate the input file names. If you do not specify the directory, tiff2mrc will use an empty string.

-in=name or -in=name_format

The first form selects a single input file to convert. The second form selects one or more files whose names correspond to a predefined template. If you have multiple files that do not correspond to one of the predefined templates, you should use the -template option which has precedence over the -in option. The allowed values for name_format are:

prefix+zt

Causes tiff2mrc to generate output file names as if "prefix_z#_t#.tif" had been selected for the name format in the user interface.

prefix+z

Causes tiff2mrc to generate output file names as if "prefix_z#.tif" had been selected for the name format in the user interface.

prefix+t

Causes tiff2mrc to generate output file names as if "prefix_t#.tif" had been selected for the name format in the user interface.

-multi=option

If you use -in to specify a single input file, use this option to control what is done if that file contains multiple images. option may be one of the following:

first

Use only the first image in the file. This is the default.

z

Treat each image as a separate z section.

t

Treat each image as a separate time point.

w

Treat each image as a separate wavelength.

-palette=conversion

Specifies how to convert TIFF files which have a color table. conversion may be one of the following:

rgb

Create an output file with three wavelengths with each wavelength corresponding to one color component (red, green, blue).

gray

Ignores the color table and creates an output with a single wavelength containing data values the raw image values from the input. This is the default.

grey

Is a synonym for the gray option.

inverted

Ignores the color table and creates an output with a single wavelength containing the contrast-reversed raw image values.

-prefix=pref

Sets the prefix to use in the input file name template. If you do not specify the prefix, tiff2mrc will use an empty string.

-t=start:end[:increment]

Sets the range of time point numbers to use when generating multiple input file names. If you omit the increment, tiff2mrc will use an increment of one if end is greater than or equal to start and use an increment of negative one if end is less than start. If you do not set a time point range, tiff2mrc will assume a range which starts at zero, ends at zero, and has an increment of one.

-template=custom_template

Sets the file name template tiff2mrc will use when generating input file names. If you specify this option, it will take precedence over a -in option.

-z=start:end[:increment]

Sets the range of z indices to use when generating multiple input file names. If you omit the increment, tiff2mrc will use an increment of one if end is greater than or equal to start and use an increment of negative one if end is less than start. If you do not set a z range, tiff2mrc will assume a range which starts at zero, ends at zero, and has an increment of one.

This example creates the file fish.dat in the current directory which contains, as time points, the images from f0001.tif through f1000.tif in /var/tmp:

    tiff2mrc -template=/var/tmp/f%4t.tif -t=1:1000 fish.dat

This example extracts all the images from exp1.tif and saves them as z sections in the MRC file exp1.mrc:

    tiff2mrc -in=exp1.tif -multi=z exp1.mrc

Topics

Overview | File Selection | Multiple Image TIFFs | Multiple Files | Palettes | Messages | Command Line