48 lines
2.1 KiB
Markdown
48 lines
2.1 KiB
Markdown
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This is a collection of tools for working with 3D image stacks of microvessel networks
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### All Dependencies (individual scripts have only a subset of these dependencies)
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* [bftools](http://www.openmicroscopy.org/site/support/bio-formats5.3/users/comlinetools/)
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* [pyxb](https://pypi.python.org/pypi/PyXB)
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* [VTK with Python Interface](http://www.vtk.org/download/)
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* [Scikit Image]
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* [VMTK](http://www.vmtk.org/)
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* [Microvessel Chaste](https://jmsgrogan.github.io/MicrovesselChaste/)
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### Working with ZEISS (IMS, LSM, CZI) Image Data
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It is useful to first extract the image metadata. This requires a copy of [bftools](http://www.openmicroscopy.org/site/support/bio-formats5.3/users/comlinetools/).
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Download it and set`$BFTOOLS_DIR` to the directory obtained after unzipping. Then do:
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```bash
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python format_conversion/extract_zeiss_metadata.py -i $IMAGE_PATH -o $OUTPUT_FILE --verbose 1
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```
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To proceed we need to convert the format to an OME TIFF and then a generic TIFF. It is easiest to work with
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one series and one channel at a time. Since we work with large images it is best to split the images into tiles and
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work in parallel.
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```bash
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python format_conversion/zeiss_to_tiff.py -i $IMAGE_PATH -o $OUTPUT_FOLDER
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```
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### Working with 3D TIFFs
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After conversion we can work with the 3D TIFFs using packages like sci-kit. It is important to remember that
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the generic TIFFs we have produced have all of their physical dimensions stripped. We do not trust any tools to
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preserve physical dimensions. The original OME metadata XML is the only reference we use.
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For easy visualization it is useful to downsample and then re-assemble the tiles.
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```bash
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python image/downsample_tiffs.py -i $IMAGE_PATH -x 3 -y 3 -z 1
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```
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### Visualizing
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We can use FIJI or VTK to visualize. VTK is nicer, but struggles with full resolution datasets. We can downsample
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as described previoulsy and then create VTK files for use in paraview.
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```bash
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python format_conversion/tiff_to_vtk.py -i $IMAGE_PATH -m $METADATA_FILE -tx 1024 -ty 1024 -dx 3 -dy 3 -dz 1
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```
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Even with this it is difficult to make nice volume renders as resource use is high. To launch a simple VTK window do:
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