For several reasons it can be helpful to be able to select only a range of images within the image stack in TrakEM2. For example to link those images in order to manually rotate them (see here). A selection of images is done via “right-click in canvas” –> Selection –> Select all that match Start and […]
Author: Stefan
Read out file names of a folder (Mac & PC)
In order to be able to quickly put together multiple file names for a .txt import of images for TrakEM2 (without typing all file names) for example, the two following processes can be used. On a Mac: mark all files in the folder, right click & copy and paste it to a .txt file or […]
Reading out folder locations and file paths the fast way
Sometimes one needs the specific location of a file or folder in order to point macros or programs towards a clear defined path. This can be done in many ways, however the easiest is to open the terminal and drag and drop the folder or file onto the terminal window: et voila, the file path […]
Opening Amira Label files in FIJI
The import from Amira label files in Fiji allows to access these files without possessing an Amira license (e.g. after a lab change) and to use the labels either in TrakEM2 to plot them on your original data stack (see here) or for general image analysis purposes directly in Fiji. Under “File –> Import” you […]
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 […]
Re-orientate images or complete stacks in TrakEM2
After aligning all images in TrakEM2, the object of interest might be positioned in an oblique angle. The orientation can be easily be changed. If the whole stack should be rotateted, make sure that all images are linked ( chain sign in the image bar on the left). If the images are not linked, only […]
Testing different CLAHE parameters on a single image
In order to avoid tediously manually testing different possible combinations of input parameters for the CLAHE filter, the following Fiji macro can be used to get a fast overview. Input image: Result:
Restricting the alignment to a region of interest in TrakEM2
After a first rough alignment (see here), it makes sense to start a second run only using a region of the stack containing the object of interest in all images. By this, the number of detected features will automatically increase even if the standard preset settings are used. Use the rectangle tool (upper left) to […]
Applying & removing image filters in TrakEM2
Image Filters are quite handy in TrakEM2 for example to increase the contrast (by using the CLAHE filter for example) in order to gain more features that can be used in the automatic alignment, or to homogenize images. The important point is, that the filters are only applied onto the mipmaps (kind of “preview” images […]
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