Process ‣ Math ‣ Image Calculator… is used to combine two images in various ways. I would happily apply Edit ‣ Invert to an 8-bit image.įor anything else, I’d generally rather convert to 32-bit and multiply by -1 – so that I know the results should be repeatable, regardless of brightess & contrast settings. I personally dislike this unpredictable weirdness. whatever maximum is set in the Image ‣ Adjust ‣ Brightness/Contrast… dialog box.Ĭonsequently, inverting a 32-bit image can give different results each time it is applied if the contrast settings are not kept the same! I only know about this sneaky alternative option through the ImageJ release notes.įor 32-bit image inversion, the pixels are subtracted from the display maximum, i.e. Since ImageJ v1.53k, the maximum value of 65535 is used… unless you happen to have a different Unsigned 6-bit range value specified via the Set button via the Brightness & Contrast dialog. This is also true for stacks: the maximum value in the entire stack is found. When I first wrote this question, to invert a 16-bit image pixel were subtracted from the maximum value within the original image. Many point operations for single images are found in the Process ‣ Math ‣ submenu.Īt the top of the list come the arithmetic operations: Add…, Subtract…, Multiply… and Divide….
So you should always at least consider converting. This isn’t always essential, but we will soon see examples where the type of the image makes a difference to the result. The second thing I often do when processing an image in ImageJ is to convert it to 32-bit floating point, using Image ‣ Type ‣ 32-bit. If you suspect you might regret a processing step, then it’s best to always duplicate the image beforehand with Shift+ D. In general, it’s left up to the user to decide when duplicating is necessary. ImageJ provides some very limited undo support for 2D slices, but it’s best not to rely on it.
Imagej software software#
When it comes to image processing, undo effectively requires the software to quietly duplicate the pixel values of an image before any processing step, so that they can be recovered later if needed.īut for big images (say, 1 GB or more), duplicating that much data could significantly slow down the software and potentially result in lots of out-of-memory errors. Implementing ‘undo’ in software is quite tricky.Įspecially in flexible software that enables the user to do a lot of different things. I frequently use duplication as a way to extract the channel from an image, as a more convenient alternative to Image ‣ Color ‣ Split Channels. This is controlled both by any ROI and by selecting subsets of channels, z-slices or time points where relevant. When working with an image in ImageJ, I almost always have at least one duplicate lingering around for when when things inevitably go wrong.īut Image ‣ Duplicate… has an extra, hidden bonus: it’s supports extracting just a part of the image.
Mistakes happen, and Edit ‣ Undo is rather limited it can undo some processing steps applied to a single image slice, but not always… and it can’t undo operations applied to image stacks We often want to process duplicates of an image in different ways, and then combine or compare the results. This applies the command Image ‣ Duplicate….īeing able to quickly duplicate an image matters for two main reasons: One of the most important ImageJ shortcuts to learn is Shift+ D to duplicate the image.
Imagej software how to#
Before we begin #īefore we embark on processing pixels, there are a couple of things we need to know how to do in preparation. It shows where to find the main point operations, including some tips (and warnings) about their use, along with a few exercises to try them out. This section introduces image processing with ImageJ. ImageJ: Point operations # Introduction #
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