/parsetrakem2

Python code for parsing TrakEM2 files.

Primary LanguagePythonMIT LicenseMIT

parsetrakem2

Python code for parsing TrakEM2 files. The code is intended to link TrakEM2 data with wormwiring.org data.

Installation

Clone or download respository. Make sure to maintain the relative paths.

Prerequisites

Python3 will need to be installed along with the following python packages

Numpy v1.15.2
Scipy v1.1.0
Matplotlib v3.0.0
lxml v4.2.5
multiprocessing-on-dill v3.5.0a4

**Note that multiprocessing appears to work on Python 3.5 but not on 3.6 and 3.7. So keep this in mind when choosing a python version.

Usage

The following outline the included scripts and provide instructions of basic usage. For more detailed documentation, run scripts with -h flag or consult the source code documentation. Main scripts are located in trakem2/. Test scripts are located in test/.

Measure adjacency

To measure adjacency of segmented TrakEM2 file use measure_adjacency.py:

python measure_adjacency.py /path/to/trakem2.xml /path/to/output.xml

Adjacency data is written to an xml file which can be easily updated. Script can be run in parallel over muliple CPU(s).

Convert xml output to csv

For convenience, the xml2csv.py will convert the output xml from measure_adjacency.py to csv format:

python xml2csv.py /path/to/xml /path/to/csv

Format of the csv is as follows:

cell_1,cell_2,index_1,index_2,layer_name,adjacency_length

Set area list colors

To change colors of area lists in a TrakEM2 file.

python set_class_colors.py -t ../data/trakem2_n2u/n2u_vol.xml -n ../mat/neuron_category_pub.txt -c ../mat/color_code.txt -o ../data/trakem2_n2u/n2u_brittin.xml

where the neuron category files has the format

cell_name,cell_class

and the color code file has the format

cell_class,html_color

**Note that the output xml file will not have the proper header for TrakEM2 to read the file directly. In linux you can cat the header as follows

cat /mat/header.txt output.xml > trakem2_readable.xml

where output.xml is the output file produced by this script and trakem2_readable is the file read by trakem2.

Author

  • Christopher Brittin - Initial work - cabrittin

License

This project is licensed under the MIT License - see the LICENSE.md file for details