I have been looking for months for a solution to image stitching. Tried many commercial softwares, but none did a good job. During all this time I carried out the stitching manually (tens of hours). And finally here I am, the solution that actually works!!! Thank you very much for putting this video out and save me many hours of dull work!
We're not sure what you mean exactly by a multipage tiff. Stitching with a z stack tiff file in Fiji works well. We suggest you open your image in Fiji without trying to stitch and see how it’s displayed. If it’s incorrect, reorder the stack (Image - hyperstack - reorder hyperstack) and save it as a new file. Do this for all files as necessary, then try to stitch the new files using grid/collection stitching.
@@StowersInstitute multi-page TIFFs have been part of the TIFF 6.0 spec since 1992. It's how the TIFF container holds the image data. Regardless, it doesn't work. When I load one of my multi-page tiffs in Fiji, it shows a single window with Z slices and a slider. I can scroll through the stack just fine. Then I have about 30 of these images (each as a multipage TIFF stack) to stitch into a huge single image with 6x5 tiles (& Z). Then, that 180 times over for my T=0 to 180 time series. I'll try load/save the images I guess.
@@KieranShort I understand now what your dataset is. Given that there are a number of dimensions in multi-page tiffs including position, for example, we wanted to verify that your data is in the right format. Stitching multiple tiffs that are z stacks should work. As stated before, in a worst-case scenario, saving out each time point as a separate series of images to stitch and then reassembling after the fact will work. Alternatively, it sounds like your image files are quite large. Fiji will need to load all of them into memory at the same time in order to stitch them together. Does your system have enough RAM for this? Assuming it does, this process will take a very long time. You can monitor what Fiji is doing through plugins - utilities - Monitor Memory. This is a running line plot of Fiji’s memory usage which will help you determine if Fiji is working on the stitching or is locked up. Thank you for your questions!
Hi, do the files need to be tif? is it possible with JPG? I got some stitched imaged but not quite good yet. I have 4 pictures to stich, each one from a circle divided in 4 quadrants. The overlapping region seem to have a repeated part. I would really appreciate your advice on this. Thank you
Thank you for the tutorial! Is there a tutorial for stitching images with unkown order? I have tried many times but the stiched image comes up all blurred and mixed, I have no way of knowing the order of the images
The shading observed in our example is due to uneven illumination contained in the data set. This is a common problem and is especially true in spinning disc images. There are two immediate ways to fix the issue, background subtraction or increased tile overlap. Before stitching, apply a background subtraction to each image individually, then stitch the background subtracted images. Another way to eliminate the illumination is to collect a blank image or average many images together to create an image of only the field (no sample structures) and then use this image to correct each image before stitching. Finally, for future data sets, you can increase the overlap between images significantly. This will increase your imaging time and number of files, etc.
Hello sir, thanks for the content. I have a problem with the stitching: I have several .tif images that are loaded correctly, but then Fiji only takes the first one into account. As a result, I obtain only one repeated image at the end. Any suggestions?
Hello, please take a careful look at the log window where it shows each image loading. Is each file truly a different name? The type of error you’re seeing usually occurs when the iterator isn’t properly set. The plugin will just load the same image over and over again. This won’t throw an error in the log window and the plugin will run normally, but only with one image. The only way to know is to look at the full path and filename of each image that’s loaded and verify that they are indeed all different images. Thanks!
Thank you for your instructive video. I successfully stitched my images but still found dark area close to the stitch lines. Is there any tips to remove these lines?
I can think of two possibilities that you are seeing. In the first, there are tile positions missing from the stitched image. In this case that entire tile position will be exactly zero at all pixels. This will happen if there is nothing in that tile position that can be registered to it’s neighboring tiles. In that case, it simply leaves that tile position out. There really is not a way to fix this. In a second case, you may be seeing striping along the X and Y dimensions of every tile. This could be due to non-uniform background. In this case, you can perform a background subtraction to make the background more uniform and therefore eliminate the striping.
Hi. Thanks for the tutorial. However, I'm having problem in choosing images that I want. I can't click 'choose' from the browse section eventhough the images are in tif format. Do you have any idea why?
If I’m understanding correctly you are clicking browse on the directory window. This is actually selecting a directory of images to try to stitch. So through this window you cannot select any individual file, you are only selecting the directory where the data is. It’s easier to copy and past the directory path into that line, than to select the directory through the browse button.
@@StowersInstitute Do you know how to apply this on mac? Mac do not display directory as windows did, but I managed to copy the location of the folder and paste it on the directory window. Still, Fiji can't find the file. Not sure if I'm doing it right though.
Is there a simple way to just stich two images together? I had to split all my SEM Images due to size before exporting and would like them together as one for editing again (there is 0 overlap). I was told i can do this with ImageJ. This method shown here sadly doesnt seem to solve the issue.
We're not sure what is going on with your Fiji installation and what you have or haven’t done. If you start with the UA-cam videos from part 1, it will cover how to set up Fiji to get all the plugins we will use. In the end, the grid/collection stitching should be able to stitch the data if there is overlap between the two images.
Thank you Thank you Thank you Thank you Thank you Thank you!!!! My Masters' thesis will be complete because of this!
I have been looking for months for a solution to image stitching. Tried many commercial softwares, but none did a good job. During all this time I carried out the stitching manually (tens of hours). And finally here I am, the solution that actually works!!! Thank you very much for putting this video out and save me many hours of dull work!
How can you get this to work, if your Tiffs have embedded Z stacks (multipage tifs)? It doesn't seem to be fusing in my hands when I do it.
We're not sure what you mean exactly by a multipage tiff. Stitching with a z stack tiff file in Fiji works well. We suggest you open your image in Fiji without trying to stitch and see how it’s displayed. If it’s incorrect, reorder the stack (Image - hyperstack - reorder hyperstack) and save it as a new file. Do this for all files as necessary, then try to stitch the new files using grid/collection stitching.
@@StowersInstitute multi-page TIFFs have been part of the TIFF 6.0 spec since 1992. It's how the TIFF container holds the image data. Regardless, it doesn't work. When I load one of my multi-page tiffs in Fiji, it shows a single window with Z slices and a slider. I can scroll through the stack just fine. Then I have about 30 of these images (each as a multipage TIFF stack) to stitch into a huge single image with 6x5 tiles (& Z). Then, that 180 times over for my T=0 to 180 time series.
I'll try load/save the images I guess.
@@KieranShort I understand now what your dataset is. Given that there are a number of dimensions in multi-page tiffs including position, for example, we wanted to verify that your data is in the right format. Stitching multiple tiffs that are z stacks should work. As stated before, in a worst-case scenario, saving out each time point as a separate series of images to stitch and then reassembling after the fact will work. Alternatively, it sounds like your image files are quite large. Fiji will need to load all of them into memory at the same time in order to stitch them together. Does your system have enough RAM for this? Assuming it does, this process will take a very long time. You can monitor what Fiji is doing through plugins - utilities - Monitor Memory. This is a running line plot of Fiji’s memory usage which will help you determine if Fiji is working on the stitching or is locked up. Thank you for your questions!
Hi, do the files need to be tif? is it possible with JPG? I got some stitched imaged but not quite good yet. I have 4 pictures to stich, each one from a circle divided in 4 quadrants. The overlapping region seem to have a repeated part. I would really appreciate your advice on this. Thank you
Thank you for the tutorial! Is there a tutorial for stitching images with unkown order? I have tried many times but the stiched image comes up all blurred and mixed, I have no way of knowing the order of the images
What are "the other tricks" you mentioned?
Thanks. It was very helpful
Thanks! Solved a stitching problem I was having!
As you can see in the example images, you get these dark lines in the middle of the image afte stitiching. How do you take care of that problem?
The shading observed in our example is due to uneven illumination contained in the data set. This is a common problem and is especially true in spinning disc images. There are two immediate ways to fix the issue, background subtraction or increased tile overlap. Before stitching, apply a background subtraction to each image individually, then stitch the background subtracted images. Another way to eliminate the illumination is to collect a blank image or average many images together to create an image of only the field (no sample structures) and then use this image to correct each image before stitching. Finally, for future data sets, you can increase the overlap between images significantly. This will increase your imaging time and number of files, etc.
Hello sir, thanks for the content. I have a problem with the stitching: I have several .tif images that are loaded correctly, but then Fiji only takes the first one into account. As a result, I obtain only one repeated image at the end. Any suggestions?
Hello, please take a careful look at the log window where it shows each image loading. Is each file truly a different name? The type of error you’re seeing usually occurs when the iterator isn’t properly set. The plugin will just load the same image over and over again. This won’t throw an error in the log window and the plugin will run normally, but only with one image. The only way to know is to look at the full path and filename of each image that’s loaded and verify that they are indeed all different images. Thanks!
Thank you for your instructive video. I successfully stitched my images but still found dark area close to the stitch lines. Is there any tips to remove these lines?
I can think of two possibilities that you are seeing. In the first, there are tile positions missing from the stitched image. In this case that entire tile position will be exactly zero at all pixels. This will happen if there is nothing in that tile position that can be registered to it’s neighboring tiles. In that case, it simply leaves that tile position out. There really is not a way to fix this. In a second case, you may be seeing striping along the X and Y dimensions of every tile. This could be due to non-uniform background. In this case, you can perform a background subtraction to make the background more uniform and therefore eliminate the striping.
@@StowersInstitute Thank you for your feedback!
Hi. Thanks for the tutorial. However, I'm having problem in choosing images that I want. I can't click 'choose' from the browse section eventhough the images are in tif format. Do you have any idea why?
If I’m understanding correctly you are clicking browse on the directory window. This is actually selecting a directory of images to try to stitch. So through this window you cannot select any individual file, you are only selecting the directory where the data is. It’s easier to copy and past the directory path into that line, than to select the directory through the browse button.
@@StowersInstitute Do you know how to apply this on mac? Mac do not display directory as windows did, but I managed to copy the location of the folder and paste it on the directory window. Still, Fiji can't find the file. Not sure if I'm doing it right though.
Is there a simple way to just stich two images together? I had to split all my SEM Images due to size before exporting and would like them together as one for editing again (there is 0 overlap). I was told i can do this with ImageJ. This method shown here sadly doesnt seem to solve the issue.
We're not sure what is going on with your Fiji installation and what you have or haven’t done. If you start with the UA-cam videos from part 1, it will cover how to set up Fiji to get all the plugins we will use. In the end, the grid/collection stitching should be able to stitch the data if there is overlap between the two images.
Could you let me know where I can download the plugin?
Hello Blanca, for instructions on how to download plugins, be sure to check out the first video in the series: ua-cam.com/video/4CkRX1KPaCs/v-deo.html
thank you!
thank you
This plugin struggles with large tiles, at least in my hands. Anybody else?
Yup