Fiji.wiki

Each dataset's stack of images consists in 268 2D images that together form a 3D image. NeuroGPS needs an input of a singular 3D image, so it's necessary to put together the 268 2D images to create a unique 3D image. This operation has been completed thanks to the software Fiji, that is a an image processing package, a "batteries-included" distribution of ImageJ, bundling a lot of plugins which facilitate scientific image analysis (Fiji website). So, the following operations must be performed:

1. Download Fiji (click here).
2. Drag and drop the 268 2D images of a dataset's stack in Fiji.
3. Click on the "Stk" button in the menu bar, than "Convert Images to Stack".
4. Save the resultating 3D image .tiff file.
5. Repeat these operations for each stack of images in the dataset.

The .tiff file created with Fiji will be the input for NeuroGPS to automatically find the neurons in the correponding stack.

A 3D images stack obtained with Fiji visualized in Vaa3D.