Grid/Collection Stitching Error

Hello,

I have used the Stitching tool by Preibisch et al. several times in the past on tiled images obtained from Zeiss and Olympus LSMs, I remember it being very foolproof to use. Now I am trying to use it to stitch tiles obtained on a Nikon C2 Confocal, and cannot find a combination of baked-in parameters that will allow me to generate a tile, instead I get the following directory error:

ERROR: Error: No correlated tiles found, setting the first tile to (0, 0, 0).

I found this error code on the old ImageJ google groups from 2012 / 2013, but it was the result of an internal bug. Does anyone have any input on why I might be receiving this error code? I have updated and reinstalled Fiji with no success. Thank you!

Best,
Michelle

Hey @MK_UVM,

In case you’re not aware of it, let me point you to a great new tool by @hoerldavid (from @StephanPreibisch’s lab) called BigStitcher that you should try. The user documentation is quite good.

Regarding your issue in particular, there’s some information that will help us figure out what’s going on:
How many tiles are there? and how are they arranged (e.g. how much overlap?) What do they look like - if you can post, say, two or three tiles here it would help.

John

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Hi John,

Thanks so much for your fast reply, and for your suggestion that I try BigStitcher. Apologies for my delayed response, I was attempting to learn and use BigStitcher - unsuccessfully, unfortunately, which I’m still trying to determine the cause of.

Regarding the error with the Grid/Collection stitching tool error, I am trying to stitch a 4 x 4 grid of 16 tiles, each with two channels (EGFP and DAPI). They were imaged using a tiling feature with 10% overlap and are labeled with their positions (tile_x001_y001.tif; tile_x001_y002.tif, etc.). The images are brain tissue, taken with a 10X air objective across the midline of a coronal slice. The errors that I’m seeing suggests that the tool cannot detect the ascending file numbers, changing the file names does not help. Another error message that I keep getting with this dataset is:
ERROR: Error during tile discovery, or invalid grid type. Aborting.

tile_x001_y001.tif
tile_x001_y002.tif
tile_x001_y003.tif
tile_x001_y004.tif

I’ve attached a few images if that will be helpful, any input you may have would be greatly appreciated.

All the best,
Michelle

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Hey Michelle (@MK_UVM ),

No problem. Sorry Bigstitcher isn’t working out for you so far. Feel free to make a new post detailing your issues if you want to pursue it further.

For the Grid stitching plugin, I ran into the same issues using the default plugin parameters. But found something that seems to work.

First, I changed the Image properties for all images so they have 2 channels and 1 slice.
Then I fiddled with the parameters a bit (see below). Give it a try and hope it works for you.

Good luck,
John

Plugin parameters:


Result:

Thank you so much for your help with this John!

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