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tiff_to_nii.rst

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Tiff to Nifti

Function to convert Tiff images to Nifti format for analysis or visualization.

GUI

Run:

$ miracl conv tiff_nii

The following window will open:

image

Click on Select Input tiff folder to choose the input tiff folder:

image

Next set the desired parameters or use the default by leaving the fields blank:

Parameters Description Default
Out nii name Output file name. clarity
Downsample ratio Downsample factor for nifti images. 5
chan # and prefix Use if tiff files have more than one channel. For example, given the names 10-04-06_R923_06R1ca_647_100p350_na144_UltraII_**C001**_xyz-Table Z1284.ome.tif for channel 1 and 10-04-06_R923_06R1ca_647_100p350_na144_UltraII_**C002**_xyz-Table Z1284.ome.tif for channel 2 with the latter being the desired channel for conversion, chan # would be 2 and chan prefix would be C00. Not invoked if not provided
Out chan name Output channel name. eyfp
Resolution (x,y) Original resolution in x-y plane in um. 5
Thickness Original thickness (z-axis resolution/spacing between slices) in um. 5
center Center of Nifti file. 0 0 0

Downsample in z

Down-sample in z dimension. Binary:

  • 0 (no)
  • 1 (yes)

1

Prev Downsampling

Previous downsample ratio if already downsampled. Accepted inputs are:

  • 0 (downsampled)
  • 1 (not downsampled)

1

After choosing the parameters press Enter to save them then Run to start the conversion process.

Tip

After the conversion is done, nifti (nii/nii.gz) files can be visualized using the ITKsnap software

Command-line

Usage:

$ miracl conv tiff_nii -f [ Tiff_folder ]

Example:

miracl conv tiff_nii -f my_tifs -o stroke2 -cn 1 -cp C00 -ch Thy1YFP -vx 2.5 -vz 5

Required arguments:

-f dir, --folder dir  Input CLARITY TIFF folder/dir

Optional arguments:

-d, --down           Down-sample ratio (default: 5)
-cn, --channum       Chan # for extracting single channel from multiple channel data (default: 1)
-cp, --chanprefix    Chan prefix (string before channel number in file name). ex: C00
-ch, --channame      Output chan name (default: eyfp)
-o, --outnii         Output nii name (script will append downsample ratio & channel info to given name)
-vx, --resx          Original resolution in x-y plane in um (default: 5)
-vz, --resz          Original thickness (z-axis resolution / spacing between slices) in um (default: 5)
-c [ ...], --center  [ ...]
                     Nii center (default: 0,0,0 ) corresponding to Allen atlas nii template
-dz, --downzdim      Down-sample in z dimension, binary argument, (default: 1) => yes
-pd, --prevdown      Previous down-sample ratio, if already down-sampled
-h, --help           Show this help message and exit