CeLaVi tools

Available tools

• mamut_to_celavi: A python executable for converting a MaMuT xml to CeLaVi json/csv.

Getting Started

Prerequisites

Python3 + pip

Clone

git clone https://github.com/ksugar/celavi-tools.git

Installation

Run the following command at the root directory of thie repository.

pip install -U .

Usage

mamut_to_celavi mamut.xml tree.json 3D_cells.csv

# usage: mamut_to_celavi [-h] input json csv
#
# positional arguments:
#   input       MaMuT xml file to convert
#   json        JSON file to output trees
#   csv         CSV file to output cells
#
# optional arguments:
#   -h, --help  show this help message and exit

Notes

branch lenghts mode

Please specify the absolute mode for importing into CeLaVi.

did format

The did for CeLaVi is generated as "ID_ID _name" using the Spot attribute in the MaMuT xml.

<Spot ID="100" name="abc" POSITION_X="1.0" POSITION_Y="1.0" POSITION_Z="1.0" FRAME="0" POSITION_T="0.0" QUALITY="-1.0" VISIBILITY="1" RADIUS="1.0" />
<Spot ID="101" name="abc" POSITION_X="2.0" POSITION_Y="2.0" POSITION_Z="2.0" FRAME="1" POSITION_T="1.0" QUALITY="-1.0" VISIBILITY="1" RADIUS="1.0" />

will generate the CeLaVi nodes with the following dids.

ID_100_abc
ID_101_abc

License

Apache-2.0 License.

Related projects

• MaMuT
• CeLaVi