Image Scalings

Set the image properties (scaling informations, color channels)

Choose the option Image scalings in fishfeats main step choices interface to do this step. (1)

  1. This step is loaded by default when you open the image on which to work on.

start_scale_anoot

On the right panel, you have a parameter dialog called Scale on which you can set-up the image global parameters:

  • scaleXY: the size in µm of 1 voxel in the XY direction.

  • scaleZ: the size in µm of 1 voxel in the Z direction.

  • direction: direction of imaging- if junctions are above the nuclei when you move in Z, then select top high z, otherwise if the junctions are towards the smaller z, select top low z

  • junction channel: the number of the color channel that contains the junction staining. The number is indicated in the name of each layers to the left panel: originalChannel0, originalChannel1...

  • nuclei channel: the number of the color channel image that contains the nuclei staining.

Channel separation

If the nuclei staining is in the same channel as the junction staining, put the same values for the two parameters and the program will separate the two signals later on. If not, be sure to put different numbers, otherwise it will try to separate the two stainings.

The plugin reads the metadata of your image and will prefill the scaling parameters based on that. However, there can be some mistakes depending on the metadata format, so it's important to always check that the scaling is correct.

A configuration file is created in the results folder when you launch the pipeline. It records some information on your current step and the parameters that you selected. If you quit the plugin with the option Quit plugin it will then save this file that can be read the next time you use fishfeats on the same image. It will then pre-select the parameters to the ones you filled in the first time. The recorded file is saved in the results folder, named as the image but with a .cfg extension.

Click Update when you have selected all the parameters to choose the next analysis step to perform.