There are two ways to extract the edge coordinates of an region of interest (ROI): 1) The long wayBefore starting to draw the region of interest (rectangle tool) and exporting the images (export –> make flat image), we start the macro recorder (FIJI Side bar: Plugins –> Macro –> Record), which allows to read out […]
export
Exporting image stacks from TrakEM2
Exporting aligned image stacks from TrackEM2 ist an important feature, allowing it to make use of semi-automatic segmentation tools available in others Open Source Software packages (such als MIB, Drishti, Ilastik…) as well as commercial packages (Amira, Imaris, VGstudio…).The export ist easily done after the alignment (see here), either as export of the complete canvas (everything visible in the […]
Export 16bit images from TrakEM2
Natively, TrakEM2 is only able to export 8bit images via the “Make flat image” function. However, 16bit images can be exported using the following small script. If only the image part below a ROI should be used for the export, use the following script (notice that you have to change the folder path (targetDir). Source