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The CA1 area in each image was manually outlined and the positive somata were removed by manual editing.
Individual autoradiographic sections are finally manually outlined and stored as individual sections (see figure 1.A) using tiff format.
First, the compartments were manually outlined and average fluorescence intensities were determined using in-built functions of ImageJ software (NIH, USA).
For CT scan analysis each lung image was manually outlined and analyzed by a dedicated software.
For each condition, 30 to 60 cells were manually outlined and projected cell area was measured.
Regions of interest (ROI) for all transverse slices were manually outlined and the surface area determined by counting the number of pixels enclosed by the ROI.
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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.
Briefly, the hippocampal formations were manually outlined (red and green Region of Interest-ROIs), and a midline (yellow) was automatically calculated.
Wings were then divided into 12 regions using the landmarks shown in Fig. 2. Region area was calculated from landmark coordinates or manually outlined (regions 5 and 9) to exclude the stigma and include the wing margin curvature.
Automated image registration eliminates the subjective manual slice-matching and manually outlined ROIs are required only once.
The LV epicardial borders, and the LV and RV endocardial borders were manually outlined in end-diastolic and end-systolic frames.
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