How to stitch .lsm in Fiji?

Hi all. I have .lsm taken using Zeiss. I have tile scan with 15% overlap. How can I stitch in Fiji automatically?


You could try Grid Collection Stitching in FIJI. For more details on usage check this page:

Good luck!

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Or you can try which is the successor of the above mentioned Grid Collection plugin.

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Hi Gayathri
Thanks for the reply. I tried Grid Stitching first. However, it requires the images to be saved in individual file and manually entering overlap percent. My files are saved in one .lsm. I was wondering whether there is an easier way. I tried to extract the tile scan and overlap information from metadata. However it seems that .lsm doesn’t contain those information.

The easiest option is getting it from the metadata.
In my experience file formats like .lsm are relatively good when it comes to such data.

In the Grid Collection Plugin you will find an option for doing this with multiseries files. Choose from the drop down menus of the plugin:
Type: Positions from file.
Order: Define by image metadata.
Press ok you will see that you can input a multi series file.

In the past this worked very nice for Zeiss files for me.


Hi Chris
Thanks for the reply. Unfortunately, I don’t see the information of Type and Order in the most recent Grid Collection.

Hi @young_madison,

What do you see when you first select the plugin? It should be this window which has the options that @schmiedc described.


Sorry for the late reply. I indeed saw that appearing in my window and the images got stitched. However, unfortunately, it was stitched incorrectly. So I ended going back to use zeiss software to stitch the fifles.

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