![]() ![]() In the resulting Concatenator window, you can check the box to include All open windows, or add and sort the desired stacks in the correct order using the drop down menus. To combine multiple small stacks into one select Image -> Stacks -> Tools -> Concatenate. This allows the stack to split into multiple equal parts. ![]() Note: The smaller stacks must be of equal size, so you need to enter a number divisible by the total number of slices. You can split a stack into smaller parts by selecting Image -> Stacks -> Tools -> Stack Splitter.Įnter the number of smaller stacks you wish to split into and select OK. You can also select Reverse (6) to reverse the order of the entire stack. Always scroll to the slice you want to change before selecting an option. ![]() Other options include duplicating a slice (4) or inserting a new image into the stack from a file (5).Īll of these commands will act on the current slice in the stack. You can also select First (2) or Last (3) to move the current slice to the front or back of the stack. You can then move a slice forwards or backwards using the arrows (1) in the options box. Go to Image -> Stacks -> Tools -> Stack Sorter. You can also rearrange the order of slices in a stack using the Stack Sorter tool. Slice Keeper and Slice Remover are fairly interchagable and ultimately serve the same function. Enter your numbers and select OK to generate the new stack. As with slice keeper, you can also use Increment to remove every 2nd, 3rd, 4th, etc slice from the stack. The Slice Remover will prompt you to nominate the slices you wish to remove from the stack, by number. Slice Remover is found on he same menu as Slice Keeper. You can also use Increment to keep every 2nd, 3rd, 4th, etc slice from the stack. Slice Keeper will ask you to nominate the slices you wish to keep in the stack, by number. Slice Keeper is found under Image -> Stacks -> Tools. You can also add and delete multiple slices using the Slice Keeper or Slice Remover tools. Selecting delete slice will remove the current slice from the stack. Selecting add slice will insert a new blank/black slice into the current stack position. To add or delete slices from a stack, navigate to the slice you want to modify and go to Image -> Stacks, and select the desired option. You can alter the slices in a stack by adding, deleting or rearranging them. When you are happy with your options, click OK to duplicate. Use these options to duplicate multiple slices or the entire stack. However, in the Duplicate window you will now have more options, where you select Duplicate Stack and can also nominate spceific slices to be duplicated intot he new stack. This can be useful if you want to extract a slingle slice from your stack for display or analysis purposes. When using Duplicate for a stack, only the current slice will be duplicated as a single image. Select your stack and follow the menu or shortcut to Duplicate as previously shown. You can use the Duplicate function for stacks also. To reverse this and generate multiple single images from a stack go to Image -> Stacks -> Stack to Images. To keep the original images select the box next to Keep Source Images. You can give the stack a new name, or keep the generic ‘Stack’. To create a stack from multiple individual images go to Image -> Stacks -> Images to Stack.Īn options window will open. You can monitor the slice number in the image information at the top left of the image window. You can also click on the left (2) and right (3) arrows to move the stack by 1 slice or click the play button (4) to run through the stack slices automatically. You can easily move through the slices in a stack using the bar at the bottom of the image.Ĭlick and drag the slider (1) to move through the stacks. The image NeuralTube.jpeg along with its individual channels and image stacks RGBStack.tif and MovieStack.tif will be used for demonstration throughout this section. More detailed informaiton on working with multiple dimmensions in imaging and stacks is covered in FIJI Intermediate. This section goes through the tools and methods for working with image stacks. You can also generate a stack yourself from related TIFF or JPEG images. When channel, Z-series or time information is recorded the images are usually opened as stacks automatically when bio-formats importer is used to open the files. Stacks can represent different channels from the same image, z-slices captured on the microscope or time series. Image stacks are composed of a number of related images opened on top of each other in a single window. ![]()
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