Quickstart

After installing precon3d into your local python enviroment (either clone through git or use pip), follow the instructions below to begin processing data.

Using Fiji (Fiji Is Just ImageJ): Some configuration files will have an entry for your Fiji app (when a Fiji subroutine is used). For Windows, use the path to fiji.exe and for Macs, use the path to the Fiji.app/fiji.

The outline below will give you the general steps for preparing a 3D reconstuction of your serial sectioning data.

1. Turn the .czi image data into stitched mosiacs. See precon3d stitcher --help
2. Pad these images and downscale them so they are easier to view and manage. See precon3d post_stitch --help and precon3d downscaler --help
3. Align the downscaled images. See precon3d aligner --help

There are useful file management utilites available through precon3d utility --help