Bead List Resample

Overview

The lists of markers from the bead alignment programs do not include information about the pixel spacing or origin. Therefore, it is not possible to use a list with a resampled or binned version of the tilt series from which the list was generated. Rather than recalculate a list of markers from scratch for the altered version of the tilt series, you can use Bead List Resample to generate a new list from an existing one by transforming the marker coordinates.

As an example, assume that you have a tilt series, a.stk, with 2048 x 2048 images. For a variety of reasons, you may want to align and reconstruct a version of a.stk, b.stk, which has been binned to 512 x 512. If you then want to take the marker coordinates for the binned version, b.sl2, and refine them for aligning and reconstructing the original tilt series, you would:

Use Bead List Resample with an input file of b.sl2, an output file of a.sl2, and a sampling ratio of 4 to create a list of coordinates usable with a.stk.
Use the interactive last stage of the bead alignment programs to refine the coordinates and calculate the alignment parameters.
Use the calculated alignment parameters with the reconstruction applications to generate the reconstruction of a.stk.

Topics

Input File

For the interactive Bead List Resample, use the "Input file" field to enter the name of the unmatched (.pl, .rbl, or .sbl) or matched (.sl) marker list that you want to convert. You can use the button adjacent to the field to bring up a file browser for selection of the file.

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Output File

For the interactive Bead List Resample, use the "Output file" field to enter the name for the output parameter file. You can use the button adjacent to the field to bring up a file browser for selection of the file.

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Sampling Ratio

Let x1 be the x pixel spacing of the tilt series used to generate the input marker list and x2 be the x pixel spacing of the tilt series for which you want to generate a marker list. Then enter the ratio of x1 to x2 in the "Sampling ratio" field.

Like the other alignment and reconstruction applications, Bead List Resample assumes the pixels in the tilt series are square: i.e. the ratio calculated above will hold true for the y pixel spacing as well.

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Input Projections

In the interactive Bead list Resample, the controls immediately below the "Input projections" label control which projections are included from the input marker list. The controls are:

All: If the "All" toggle button is on, all projections from the input marker list are considered for included in the output list (for a matched list, the "Count" control for output projections may limit the total number included in the output). If the "All" toggle button is off, the "Range" and "Increment" fields described below are active and control which projections to include from the input.
Range: The first value in the "Range" field is the zero-based index of the first projection to include. The second value in the "Range" field is the zero-based index of the last projection to include.
Increment: The value in the "Increment" field is the step between adjacent projections included from the input list: for instance, use an increment of two to skip every other projection.

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Output Projections

In the interactive Bead List Resample, the controls immediately below the "Output projections" label control the output numbering for the projections selected from the input list. The controls are:

Auto: If the "Auto" toggle button is on, the projections selected from the input are numbered zero for the first projection, one for the second, and so on. If the input list is a matched list, the number of projections in the output is the minimal number necessary to cover the specified input projection range. If the "Auto" toggle button is off, the "Start", "Increment", and, for matched lists, "Count" fields described below control the output numbering for the selected input projections.
Start: The value in the "Range" field is the zero-based index for the projection in the output which is the counterpart for the first projection selected from the input list.
Increment: For input projections i and i+d where d is the input section increment, the corresponding output projection indices will differ by s where s is the value shown in the "Increment" field.
Count: The "Count" field only has an effect if the input list is a matched list. In that case, use the "Count" field to limit the total number of projections included in the output list; the projections will be numbered from zero to the value in the "Count" field minus one.

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XY Range

In the interactive Bead List Resample, the first value in the "X range" field is lower bound for the x coordinate of markers included in the output, and the second value in the same field is the upper bound for the x coordinate of markers included in the output. If the "All" toggle button immediately adjacent "X range" field is on, the values in the field are ignored and no restrictions are enforced on the x coordinates of the markers. The "Y range" controls function similarly but control the range of y coordinates accepted.

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XY Offset

The value in the "X offset" field is added to each x coordinate before scaling by the pixel spacing ratio and writing the transformed coordinate to the output list. In a similar fashion, the value in the "Y offset field" is added to each y coordinate.

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Command Line

A command-line application, tfbl, provides the same operations as the interactive Bead List Resample. To reproduce the example from the overview (calculate a bead list, a.sl2, from another bead list, b.sl2, for the tilt series at one-quarter of the resolution), use

     tfbl b.sl2 -ratio=4 -out=a.sl2

The full command-line syntax is (optional parts are shown in braces; parts to be replaced with a value appropriate for your case are shown in italics):

    tfbl input_file [-ratio=r] \
        [-istart=is] [-iend=ie] [-istep=ii] \
        [-ostart=os] [-ostep=oi] \
        [-out=out_name] [-nv=count] [-xrange=l[:u]] \
        [-yrange=l[:u]] [-xoff=o] [-yoff=o]

input_file: Is the name of the input marker list. If the name is - (a single hyphen), tfbl reads the marker list from standard input.
-ratio=r: Sets the ratio, r, of the x pixel spacing assumed for the input marker list to the x pixel spacing assumed for the output marker list. tfbl assumes that the ratio of the y pixel spacings is also r. If you do not specify a pixel spacing ratio, tfbl assumes the ratio is one.
-istart=is: Sets the zero-based index for the first projection to use from the input marker list. If you do not specify the first projection to use, tfbl will start from projection zero.
-iend=ie: Sets the zero-based index for the last projection to use from the input marker list. If you do not specify the last projection to use, tfbl will end with the highest projection index in the input marker list.
-istep=ii: Sets the index increment between adjacent projections to use from the input marker list. ii must not be zero. If you do not specify an increment, tfbl uses an increment of one.
-ostart=os: Sets the destination projection in the output for the starting projection that you selected with -istart. os is the zero-based index of the destination projection. If you do not set the destination projection, tfbl assumes that the destination is projection zero in the output.
-ostep=oi: Sets the increment between destination projections for adjacent projections taken from input marker list. If you do not set the destination increment, tfbl uses an increment of one.
-out=name: Sets the name of the file to create for the output marker list. If you use this option more than once, only the last has any effect. If you do not specify the name of the output file, tfbl writes the generated marker list to standard output.
-nv=count: If the input marker list is a matched list (.sl), sets the total number of projections (which will be numbered from 0 to count-1) in the output marker list. Has no effect if the input marker list is not matched. If you do not set the number of output projections for a matched list, tfbl uses the smallest number that will accommodate the destination projections for the projections selected from the input marker list.
-xrange=l[:u]: Sets the range of x coordinates accepted from the input marker lists. Markers whose x coordinate is less than l or greater than u will not be included in the output marker list. If you do not specify u, tfbl does not place an upper limit on the x coordinate value. If you do not set the x range, tfbl does not restrict the x coordinates at all.
-yrange=l[:u]: Sets the range of y coordinates accepted from the input marker lists. Markers whose y coordinate is less than l or greater than u will not be included in the output marker list. If you do not specify u, tfbl does not place an upper limit on the y coordinate value. If you do not set the x range, tfbl does not restrict the y coordinates at all.
-xoff=o: Sets the value, o, added to each x coordinate before scaling by the pixel spacing ratio. If you do not specify an offset for the x coordinate, tfbl uses an offset of zero.
-yoff=o: Sets the value, o, added to each y coordinate before scaling by the pixel spacing ratio. If you do not specify an offset for the y coordinate, tfbl uses an offset of zero.

Overview

Topics

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