Parameters file

All pyHiM parameters are gathered in a single configuration file called parameters.json.

This file can be edited manually or using a graphical user interface.

You can find a global description of each parameter in the reference guide.

Manually

• Copy an parameters.json file in the folder where you want to run pyHiM.

Note

A typical example can be find on GitHub

• With a text editor, update the relevant parameters. For example, the name of the referenceFiducial needs to be changed according to your experiment settings.

• The common section defines the default parameters for each label. For each label, you can personalize the value of a parameter by indicating its new value in the label section.

Example: The Z projection will be done by Maximum Intensity Projection (MIP) for all labels except for the barcode images, which will use the sum method:

    "common": {
        "zProject": {
            "zProjectOption": "MIP",
            "..."
        },
        "..."
    },
    "labels": {
        "barcode": {
            "zProject": {
                "zProjectOption": "sum",
            }
        },
        "..."
    }

Graphical user interface

You can also create and modify parameters.json with an interface. In the folder where your data are saved, launch the editor:

pyhim_parameters

Indicate your parameters and click on Save settings. An parameters.json file will be created inside your folder with the modified parameters.

Note

If you have modified an existing parameters.json, a copy of the previous version will be saved in the file named parameters_preversion.json.