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 4th 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.
The QuickNII user manual is found on https://www.nitrc.org/docman/?group_id=1341.
The basic steps are:
- Open one image 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 sectionDetermine the sectioning angles (dorso-ventral and medio-lateral)
- Save the positions