The CA1 area in each image was manually outlined and the positive somata were removed by manual editing.
For TBI contusion volume assessment, the ipsilateral and contralateral hemispheres were manually outlined.
A VOI defining each organ insert was manually outlined using the Hawkeye CT data and transferred to the SPECT image.
Both tumor and background were manually outlined on the basis of an additional [18F]FDG scan, which was performed directly after the TKI-PET scan was finished.
Infarct volumes were manually outlined on diffusion-weighted MR images by an experienced neuroradiologist using an imaging analysis tool (functool, advantage windows, version 4.3; GE healthcare).
Lung CT images were manually outlined including only lung parenchyma and excluding bronchi and big intrapulmonary vessels and analysed with a dedicated software (Maluna 3.17, University Hospital of Göttingen, Germany) to measure lung gas content (i.e. functional residual capacity), lung weight and aeration distribution, as previously described [22].
To quantify the migration rate of U2OS and PtK2 cells, cells were manually outlined using ImageJ software.
First, the compartments were manually outlined and average fluorescence intensities were determined using in-built functions of ImageJ software (NIH, USA).
The cerebrum and cerebellum were manually outlined from an anatomical image of the zebra finch brain and overlaid to our SPM images.
In each imaged slice, PNNs were manually marked and cross-sectional area of CSPG clouds, as well as the entire cross-sectional striatal area, were manually outlined (Neurolucida), and both CSPG cloud and PNN density measurements were obtained.
All neurons in each field were manually outlined using Adobe Photoshop.
