cellom2tif
==========

Fiji Jython script to convert Cellomics .C01 files to TIFF.

# Dependencies

Needs to be run through [Fiji](http://fiji.sc), not the Python interpreter.

# Usage

Be sure to download Fiji and update it (it will prompt to update upon
launch). Then:

```
/path/to/fiji /path/to/cellom2tif/cellom2tif.py path/to/c01/files output/path
```

On Mac OS X, the Fiji executable is usually at:

```
/Applications/Fiji.app/Contents/MacOS/fiji-macosx
```

On Linux, it's

```
$DOWNLOAD_DIR/Fiji.app/ImageJ-linux64
```

# Licenses

`argparse.py` is distributed under the [Python Software Foundation License](
http://opensource.org/licenses/Python-2.0).

The rest of the project is distributed under the [3-clause BSD license](
http://opensource.org/licenses/BSD-3-Clause)

# Author

Juan Nunez-Iglesias (juan.n@unimelb.edu.au), inspired by a Fiji macro from
Cameron Nowell (cameron.nowell@wehi.edu.au).

# Thanks

Albert Cardona (cardonaa@janelia.hhmi.org).


cellom2tif
==========

Fiji Jython script to convert Cellomics .C01 files to TIFF.

# Dependencies

Needs to be run through [Fiji](http://fiji.sc), not the Python interpreter.

# Usage

Be sure to download Fiji and update it (it will prompt to update upon
launch). Then:

```
/path/to/fiji /path/to/cellom2tif/cellom2tif.py path/to/c01/files output/path
```

On Mac OS X, the Fiji executable is usually at:

```
/Applications/Fiji.app/Contents/MacOS/fiji-macosx
```

On Linux, it's

```
$DOWNLOAD_DIR/Fiji.app/ImageJ-linux64
```

Note that weird behavior may occur when the input and output directories are
the same, or subdirectories of one another, since the script recurses down
subdirectories and recreates the subdirectory structure in the output path.

# Licenses

`argparse.py` is distributed under the [Python Software Foundation License](
http://opensource.org/licenses/Python-2.0).

The rest of the project is distributed under the [3-clause BSD license](
http://opensource.org/licenses/BSD-3-Clause)

# Author

Juan Nunez-Iglesias (juan.n@unimelb.edu.au), inspired by a Fiji macro from
Cameron Nowell (cameron.nowell@wehi.edu.au).

# Thanks

Albert Cardona (cardonaa@janelia.hhmi.org).


Add warning to keep in and out directories separate
Add warning to keep in and out directories separate