Piece together a few (>=2) 2D images into a full image in Fiji(imageJ)

C2-DIV3_shRNA322.lif - Image007-1.tif (768.2 KB) C2-DIV3_shRNA322.lif - Image009-1.tif (768.2 KB) C2-DIV3_shRNA322.lif - Image011-1.tif (768.2 KB) C2-DIV3_shRNA322.lif - Image013-1.tif (768.2 KB) Sample image and/or code

  • Upload an original image file here directly or share via a link to a file-sharing site (such as Dropbox) – (make sure however that you are allowed to share the image data publicly under the conditions of this forum).
  • Share a minimal working example of your macro code.


  • I am about to measure the morphology of the axons of neurons. The axons usually is too long to fit in one visual field under microscope. I tooK several images with each image contains a small part of the axon.

  • I would like to measure the length and arborization of the axons.

Challenges: is there a way to piece these images into 1 so that I can measure it in a single file instead of measure individual part of an axon and add them together?

I have tried stitching but it does apply to my images, because these images are not tile-scan images. I also read the tutorial on TrakEM2, but my images is 2D.

Hi Cai Qi,
Have you tried the Grid/Collection stitching plugin in Fiji/ImageJ by Stephan Preibisch (Grid/Collection Stitching Plugin - ImageJ)? Seems to be working for your sample images using the ‘Unknown Position’ option (see below).
Good luck,