how to slice time course in image j

What is a slice in ImageJ?

The individual images in a stack are called "slices" in ImageJ. The window's status bar shows the number of the current slice and total slices (in this case, slice 1/12 or 1 of 12), the width and height of the image in pixels, and the memory occupied by the stack, in this case 12 MB.

What is the difference between the first slice and intermediate images?

The first slice image is the whole of the original image, scaled so that it fits into the framesize of the ROI. The intermediate images are progressively scaled so that the last frame is 100%.

How to unstack the slices of an image?

To unstack the slices into separate image windows, choose Image > Stacks > Stack to Images. To unstack the slices into separate image windows, choose Image > Stacks > Stack to Images. Each slice of the stack is now in its own window.

How do I Open Week 3 in ImageJ?

Launch ImageJ by double-clicking its icon on your desktop or by clicking its icon in the dock (Mac) or Launch Bar (Win). Choose File > Open..., navigate to your Week 3 folder, and open the glacial_retreat.jpg image. Use the Rectangular selection tool to carefully select a rectangle around the 2001 (bottom) glacier image.

How do you split stacks in ImageJ?

You can split a stack into smaller parts by selecting Image -> Stacks -> Tools -> Stack Splitter. Enter the number of smaller stacks you wish to split into and select OK.

How do I add a time stamp in ImageJ?

0:284:50How to add time stamp to video in ImageJ (2 methods) - YouTubeYouTubeStart of suggested clipEnd of suggested clipThere are two ways to hard stamp to your time-lapse images it's very easy to do you can either goMoreThere are two ways to hard stamp to your time-lapse images it's very easy to do you can either go through plug-in stacks timestamper this will open this window that asks for the starting time.

How do you delete a slice in ImageJ?

Some of these functions are described below.Deleting a single slice: Image › Stacks › Delete Slice.Deleting a number of slices: Image › Stacks › Tools › Slice remover.Select the slices to remove: Image › Stacks › Tools › Make substack.Stack to images/Images to stack: Image › Stacks › Stack to images (Images to Stack…).More items...

How do you make a montage in ImageJ?

Download Image_Montage. txt to the plugins/Macros folder, restart ImageJ or click Help>Update Menus and there will be a new Image Montage command in the Plugins/Macros menu. Description: ImageMontage creates montages of images without the need to load them into a stack first.

How do I add a scale bar in ImageJ?

Add a Scale Bar With the scale set, ImageJ can now print a scale bar on the images for you. Choose Analyze > Tools > Scale Bar... and enter the settings for your scale bar. The scale bar on the image updates automatically to show you the results of your changes.

How do you add a time stamp to a movie?

How to Include the Date & Time Stamp in Movie MakerLaunch Windows Live Movie Maker and click the "Add videos and photos" button at the top of the window. ... Click the "Add Caption" button to the right of the "Snapshot" button. ... Type the date and time that you would like to add to the film.More items...

What is stack in ImageJ?

ImageJ can display multiple spatially or temporally related images in a single window. These image sets are called stacks. The images that make up a stack are called slices.

What is Z stack imaging?

Z-stacking (also known as focus stacking) is a digital image processing method which combines multiple images taken at different focal distances to provide a composite image with a greater depth of field (i.e. the thickness of the plane of focus) than any of the individual source images1,2.

How do I save a stack in ImageJ?

When the “Save As” dialog is opened, ImageJ will enter the image window's name, plus the appropriate file suffix, as the “File Name”. Animated GIF… Choosing this option from the “Save As” menu saves a stack as an animated GIF. It is only compatible on RGB or 8 bit images.

How do you stitch pictures in Fiji?

0:168:28Grid/Collection Stitching using Fiji - YouTubeYouTubeStart of suggested clipEnd of suggested clipSo I have some data sets that have tile positions all split out into a formatted array and what weMoreSo I have some data sets that have tile positions all split out into a formatted array and what we want to do is run this plugin to try to get them to stitch together.

How do you make a video with image J?

To make a movie using ImageJ:save your images in a folder: if your script saves file names without space-filling 0's (e.g. Image1. ... open the images in ImageJ: click on File>Import>Image Sequence... ... to make sure everything's ok, check the opened stack by pressing. ... save the AVI file by clicking File>Save as...>AVI.

How do I crop the same size in ImageJ?

1:1610:46How to Batch Crop Your Images in ImageJ / Fiji - YouTubeYouTubeStart of suggested clipEnd of suggested clipThe shortcut for that would be command s which would give you the option to just save this to theMoreThe shortcut for that would be command s which would give you the option to just save this to the same directory you pulled it from.

How to illustrate rapid frame to frame changes in intensity?

Rapid frame-to-frame changes in intensity (e.g. calcium “puffs” or TMRE “depolarizations”) can best be illustrated by subtracting each frame from the previous/next. Use the plugin " Delta F up ".

How to make F0 image in Fiji?

Generate an “F0” image by averaging the first few frames of the stack. This can be done with the “ Image/Stacks/Z-project " menu item (Fiji assumes stacks to be z-series rather than t-series), using the “ Average Intensity ” drop-down box option. Select “Start slice” as 1 and “Stop slice” as 5-10 depending on how many frames you wish to average. Rename the new z-projected image (“ Image/Rename ”) “Fzero”.

How to create a surface plot?

Surface plots can be generated in many ways: notably via the menu command “ Analyze/Surface plot ” or via the plugins “ SurfaceJ ” and "Interactive 3D Surface Plot ". These functions will surface-plot movies as well as single frame images. Ensure the features you’re interested in are “Contrast stretched” optimally. This can be done using a “Max intensity projection” on the stack. Get the max and min pixel intensities and apply these to the stack. Remember, do not perform intensity analysis on images that have had their contrast stretched.

Can you surface plot a movie?

You can surface plot either a single frame or a movie. Surface rendering is a slow process so it is best to pick a frame from the movie that shows the features you’re trying to demonstrate. Duplicate this ( ^ Ctrl + D) and use it as a test image to get the best settings for surface plotting your movie.

What is zoomify movie sequence?

The Zoomify plugin will generate a movie sequence such that the first frame includes the whole image and the last is the user defined ROI at 100%. The first slice image is the whole of the original image, scaled so that it fits into the framesize of the ROI. The intermediate images are progressively scaled so that the last frame is 100%. The scale factor is noted as the label slice in the stack.

How to superimpose a source?

Superimpose the source by specifying the X and Y coordinates for the location of the upper left hand corner.

Can transformj images be rotated?

Images and stacks can be resized and rotated with native functions or with the more sophisticated TransformJ set of plugins from Erik Meijering. More details about each TransformJ plugin can be found on this website.

Can you reverse image stack?

Can do reverse operation with " Image/Stack/Tools/Montage to Stack " , but will need to specify the number of rows and columns to ensure the correct number of slices.

Can slices be manipulated?

The slices in a stack can be manipulated in many ways. Some of these functions are described below.

How to correct uneven illumination in confocal microscope?

You can correct for uneven illumination and horizontal "scan lines" in transmitted light images acquired using confocal microscopes by using the native FFT bandpass function ( Process › FFT › Bandpass Filter ...).

How does ratiometric imaging work?

Ratiometric imaging compares the recordings of two different signals to see if there are any similarities between them . It is done by dividing one channel by another channel to produce a third ratiometric channel. This technique is useful because it corrects for dye leakage, unequal dye loading, and photo-bleaching. An example application would be measuring intracellular ion, pH, and voltage dynamics in real time.

What is the Z profiler?

The plugin Plot Z Axis Profile (this is the Z Profiler from Kevin (Gali) Baler (gliblr at yahoo.com) and Wayne Rasband simply renamed) will monitor the intensity of a moving ROI using a particle tracking tool. This tool can be either manual or automatic. Use the Image › Stacks › Plot Z Axis Profile command.

What is equalize contrast?

The Equalize contrast command applies a non-linear stretch of the histogram based on the square root of its intensity.

What is line scanning?

Linescanning involves acquiring a single line, one pixel in width, from a common confocal microscope instead of a standard 2D image. This is usually a faster way to take an image. All the single pixel-wide images are then stacked to recreate the 2D image.

How to correct uneven illumination?

You can correct uneven illumination or dirt/dust on lenses by acquiring a "flat-field" reference image with the same intensity illumination as the experiment. The flat field image should be as close as possible to a field of view of the cover slip without any cells/debris. This is often not possible with the experimental cover slip, so a fresh cover slip may be used with approximately the same amount of buffer as the experiment.

Can macros be used on time courses?

This macro, because it also works with stacks, can be used on time-courses with varying backgrounds.

How to launch ImageJ?

Launch ImageJ by double-clicking its icon on your desktop or by clicking its icon in the dock (Mac) or Launch Bar (Win).

How to open a stack in ImageJ?

To open a stack in ImageJ that has been saved as an animated gif, choose File > Import > Animated GIF.

How fast can ImageJ animate?

Stack windows have a scroll bar across the bottom to cycle through the slices, and you can animate the images at a speeds from one frame every 10 seconds to over 1000 frames per second.

How to save an image as an albedo?

Download the images below into the Albedo folder. Click the thumbnail to open the full size image in a larger window. Then right-click (Win) or control-click (Mac) to choose file Save Image As... Do not rename the files. Keep them as 01_albedo.jpg, 02_albedo.jpg, etc.

What are the operations that can be applied to all slices in a stack?

Many operations, such as selecting, filtering, thresholding, and contrast enhancement can be applied to all slices in a stack. To stack a set of images, they must all be the same width, height, and bit depth. The number and size of the images you can stack depend on the amount of memory in your computer. top of page.

How to import image sequence in Albedo?

Choose File > Import > Image Sequence... and navigate to the Albedo folder.

How to represent image series in printed report?

Stacks are great on your computer screen, but how do you represent the image series in a printed report? The solution is to create a montage — rows and columns of thumbnail images on a single page — to save and import into your report.

How much memory does ImageJ use?

Java applications such as ImageJ will only use the memory allocated to them (typically 640 MB) but this dialog allows the user to allocate more than the default.

How to re-adjust opacity of a blended image?

Once created, opacity of the blended image can be re-adjusted at any time using Edit▷Selection▷Properties… [y] ↑. Use Shift E ( Edit▷Selection▷ Restore Selection [E]↑) to recover the blending image after clicking outside its limits. Use Shift F ( Flatten [F]↓) to finally embed the imageROI.

How to transfer a selection from one image to another?

You can transfer a selection from one image to another by activating the image with the selection, activating the destination image, then pressing Shift E (the keyboard shortcut for Edit▷Selection▷ Restore Selection [E]↑ ). This shortcut can also be used to restore accidentally deleted ROIs. Alternative ways to transfer ROIs across images involve the ROI Manager↓ and the cursor synchronization features provided by Analyze▷Tools▷Synchronize Windows ↓.

How to fill a stack image?

With stacks, a dialog is displayed offering the option to fill the selection in all stack images. Fill the selection by pressing F to avoid this dialog.

How to clear the selection in a stack?

With stacks, a dialog is displayed offering the option to clear the selection in all stack images. Clear by pressing Backspace to avoid this dialog.

What is the invert value for an image?

For 8-bit and RGB images ( see Image Types and Formats↑ ), Invert always uses min = 0 and max = 255, regardless of the data values. For 16-bit and 32-bit images, the actual minimum and maximum are used (rather than the full range of the pixel type).

What does "0-100" mean in JPEG?

JPEG quality (0-100) Specifies the compression level used by File▷Save As▷ Jpeg…↑ Requesting a higher degree of compression (a lower value) will result in smaller files, but poorer image quality. Note that lossy JPEG compression creates serious artifacts, see 3: Image Types: Lossy Compression and Metadata↑.

When I analyze my data with Image J using just the mean fluorescence value, does it capture?

When I analyze my data with Image J using just the mean fluorescence value it does not capture differences between my treated and control cells as well as the integrated density. The treatment should not be causing a change in cell morphology.

Can you compile optical sections under a confocal microscope?

After taking microscopic images under a confocal microscope you can compiled all the optical sections in the form of a 3D image. I need to do this for a few of the stacks (sections) by taking advantage of Image J software.