Preparation of the image serie

Resize your raw 2D images to 24-bit PNG and JPEG. Images can be loaded up to the resolution of 16 megapixels (e.g.4000x4000 or 5000x3000 pixels), however QuickNII does not benefit from image resolutions exceeding the resolution of the monitor in use.

The resized files must follow the naming convention having an unique ID in the format: sXXX.., with XXX.. reflecting the serial order and spacing of the sections (e.g. s002, s006, s010 for every 4^th section starting with section 2).

Generate your images descriptor file with FileBuider

Use the small program “FileBuilder.bat” provided with QuickNII. A new window will open, and ask for the folder where your images are located. Point to the correct folder, mark all image files, and click ok. An XML file is generated. Always save this file in the same folder as the resized images.

Open QuickNII and load your images

Open the QuickNII program from the .exe file. Once the program opens, click the Manage data button and load your XML file.

A detailed QuickNII user manual as well as a demo dataset can be found on https://www.nitrc.org/projects/quicknii/

The idea is to determine the cutting angles (dorso-ventral and medio-lateral) for the whole serie as these should be consistent. Once found in a few sections, apply the same angles to the rest of the serie.

Anchoring procedure

The basic steps are:

-Open one image in the beginning of the series and use anatomical landmarks to find the approximate anteroposterior position of the section.     Select the atlas modality to be overlayed to the image (MRI, Atlas, etc..)

-The transparency slider can be used continuously to determine how well the atlas fits the section. Determine the sectioning angles (dorso-ventral and medio-lateral) by tilting the atlas and adjust the atlas borders.

-Save the positions for this section for now, you can adjust these later.

-Open the next image, located at the other end of the serie and repeat the same procedure as above i.e. find the approximate anteroposterior position of the section and test how well the cutting angles fit this section. Save the positions.

-Explore a few sections in order to find the angles fitting most sections in order to achieve a global anchoring.

-By having the same angles in these two sections (i.e. ML=+1; DV= -4), QuickNII will apply them to all other sections located in between. The antero-posterior positions of all images are also estimated.

-Review all sections, adjust atlas borders and save.

-Export custom atlas slices corresponding to your series by clicking on the “export Slices” button. The exported .flat files are used for the quantification by Nutil Quantifier.

Nonlinear adjustment with VisuAlign

A detailed VisuAlign user manual can be found on https://www.nitrc.org/docman/?group_id=1426

The basic steps are:

-Use same folder as QuickNII with your png images and series descriptor (xml file). You will need the JSON version of the descriptor (it is generated in QuickNII by clicking “Save JSON”).

-Open tool by clicking on “VisuAlign.bat” file. It loads and saves JSON files created by QuickNII.

-Add markers and drag them to move the atlas borders. Start with the borders of the tissue and then adjust internal landmarks.

NB: keep the number of markers to a minimum.

-The outline mode is toggled by pulling the opacity slider to the far right (as seen in the screenshot). A color picker to the right of it becomes active for changing outline color.

-“Debug mode” displays triangles representing the deformation field, it is enabled from the View menu (and also enables a color picker for changing the color of the triangles).

- Use the “Save As”  to save your deformations as a new JSON file.