For details about the different functions of Gimp and how to use them please refer to the documentation of Gimp at. To create such a representation of the contours in your image proceed as described below. The background of such an image is usually white and the cell boundaries are given as 1-pixel wide lines in black, or vice versa. In a contour image just the surroundings of the cells are marked. Generating/editing contour images with Gimp and MiToBo The result will be a label image which you can save to disk, e.g., in TIF format. This will bring-up a window where you can select yourīinary mask image as input image. Then select from the tree of available operatorsīy double-click. To transform this mask into a label image navigate in ImageJ/Fiji to You should now have a black-white mask image for your cell image. Proceed with all cell regions from the ROI manager that way. Now change the foreground color to white and select a cell region from This will fill your complete image in black. If ImageJ ROIs are sufficient for your task, simply save the set of contours to file by selecting from the ROI managerĪnd save the ROIs to a file of your choice.įor generating a label image, first set the ImageJ foreground color to black via Repeat the same for all other cells in the image. When done, press "t" to add the contour to the ROI manager. Use the freehand tool to surround a cell in the image. To manually label the cells in an image in ImageJ/Fiji you can proceed as follows: The outcome of the operator will be a label image which is accepted as input for most MiToBo operators requiring contour or region information. If this is not the case, invert the image using the ImageJ/Fiji function To use the operator make sure that your contours have black color on a white background. Such images can easily be converted into a label image using the MiToBo Runner to be found in ImageJ/Fiji viaĭe - unihalle - informatik - MiToBo - segmentation - regions - labeling
Refer to the documentation of the specific operator for details.Ĭontours can also be represented by line drawings, i.e., images with white (or black) background where the contours are marked as 1-pixel wide lines in black (or white). Note that some operators also accept binary masks. ImageJ ROIs: contour/region data in ImageJ ROI format.label image: an image where the background is black and each cell (or more general: foreground object) is marked with a unique gray value.Most operators in MiToBo accept cell contour information in one of the following formats:
#FIJI IMAGEJ CONTOUR MANUAL#
On this page you will find information about manually post-processing segmentation results as well as suggestions how to best perform manual segmentation.
However, if automatic segmentation does not work properly and manual post-processing is not an option, cell segmentation can also be performed completely manually. PaCeQuant includes algorithms for automatic cell segmentation, and operators like the CellBoundaryExtractor2D might be used for extracting cell boundaries. Thus, they require information about the cell regions and cell boundaries, respectively, of individual cells. Some MiToBo operators like PaCeQuant, ActinAnalyzer2D or CytoskeletonAnalyzer2D analyze individual cells in microscope images. Manual annotation and labeling of cell contours