This plugin calculates intensities (mean, min, max or sum) of the image that belongs to two materials of the opened model.
The results of the plugin may be seen on the screen of Microscopy Image Browser or saved as Excel spreadsheet.
- 1. Load images
- 2. Create a new model: press the Create button in the Segmentation Panel
- 3. Add material to the model: press the + button in the Segmentation Panel; select 1 in the Materials list, press the right mouse button and Rename it to Nucleus.
- 4. Select the Brush tool in the Selection type and draw nuclei of the cells
- 5. Make sure that the 1 is selected in the Add to list and press the A key button to add the drawn areas to the Nucleus material of the model.
- 6. Add another material to the model (the + button) and rename it to Cytoplasm.
- 7. With the Brush tool draw areas of the cytoplasm and add it to the 2 material.
- 8. Repeat 4., 5. and 7. for all slices of the opened dataset
- 9. Start NucleusVsCytoplams tool: Menu->Plugins->IntensityAnalysis->NucleusVsCytoplams
- 10. Select color channel and materials to analyze, define other parameters of the NucleusVsCytoplams tool and press the Continue buttton.
Note! Remember to save the model for future use!
- Color channel to analyze - a combo box that allows to define a color channel that will be analyzed.
- Calculate parameter - a combo box that allows to choose type of the intensity to analize (Mean, Minimal, Maximal, or Sum).
- Calculate ratio of - two comboboxes that allow to select ratio of which materials should be analyzed
- Plot ratio as histogram - the ratio between intensities will be displayed as a histogram.
- Save results in Excel format - check this to save results as Excel spreadsheet
- Filename to export - the ... button and the edit box to specify the filename for the export
Part of the code written by Gunther Struyf was used when writing this function.