Preprocessing of 3D images

Segmentation is performed on 2D images. This plugin allows to obtain 2D images from 3D images either by a projection or by saving each z-plane separately. These images are typically stored in a separate folder. 2D images by applying a projection, and these images are typically stored in a separate folder.

Install ImJoy plugin PreProcess from here.

The default settings of the plugins allow to quickly perform the recommended workflow. You only have to paste your data folder.

  1. 3D images are stored in a folder acquisition

  2. In the pre-processing step, the folder to save data is obtained with

    1. the text replacement acquisition>>analysis.
    2. Images are stored in a new subfolder segmentation-input

    With these options, the images will be saved in a folder acquisition\segmentation-input

Running the plugin

  1. Before running the plugin, you have to specify a few parameters. Note that you have to perform this projection for each channel-type. This allows to use different projection methods for a channel. This can be set in the plugin interface, avaible after clicking on the arrow down next to the plugin name.

    imjoy-preprocess

    Here the following parameters can be set.

    Option Type Default Description
    Path DATA str Full path to folder containing data to be segmented.
    Path SAVE str acquisition>>analysis Several options exist. See dedicated section here below for more details.
    Subfolder str segmentation-input Sub-folder where results should be saved (if defined)
    Channel string str dapi Unique string to identify channel that should be processed.
    Img extension str .tif Extensions of images to be loaded.
    Projection type str mean Different projection types: max, mean, indiv. The option indiv implies that a z-stack is split into individual slices, stored in subfolder for each image.
    Search recursive bool false Should provided folder be search recursively for images (true/false).

  2. Pressing the button PreProcess will start the pre-processing. Progress can be monitored in the plugin log, available by pressing on the i next to the plugin name.

  3. Results will be saved in the specified folder. For each image a json file with basic properties of the file, and an image with the same name as the original one will be saved.