At least for the system, we are on the same page. Thanks for all the other info you gave, it might be needed later. You don’t have to open it, you just need to land it in the proper place, from where ImageJ, without notifying you, will incorporate it in its list of available (plugin) commands. Good Evening (GMT+1) well, you have downloaded the file. Oh, and it takes a little effort, but writing down (in the current conversation) the exact error message is very helpful, so please take this effort. Then we can work on the privacy settings, otherwise we’ll continue to get ImageJ to accept the plugin. If so, please let me know what version of Safari (in the Safari menu, choose ‘About Safari’ you have, and see what version of MacOS you have (under the Apple menu: about this Mac). Maybe you have a new version of Safari that I don’t know yet, and that version of Safari refuses to download class files. If that button is not present, or there is no class file mentioned, try to use the right mouse button or hold the CTRL key while pressing the link, and from the menu that pops up, choose ‘Download Linked File’, which should get you that class file. Pressing the magnifying glass will reveal the file. If you click that button, a line appears with the name of the downloaded file and a magnifying glass. Safari then gives an extra button at the top-right of the window, with a dark circle and an arrow pointing down. If so, Safari should have started the download. You say you tried to download did you just click the link to the class file in this page? Let’s first make sure you have the class file on your computer.ĭownloading a file should be possible regardless of your privacy settings, which is what causes the complaint of the unapproved developer. Since you are a self-declared non-geek, we’ll take small steps.Īs we take small steps, it might take a bit longer and will give less frustration. Let’s take it step by step to get you where you want to be. Hi at least we have some objective complaints to work on. If you are not satisfied with the result, play with n try e.g. Then press OK That will generate you a nice focused image and a height map to go with it. Load your stack, choose the StackFocuser command, tick the boxes of the dialog box that opens and have 11 for n. Now you have an extra command in the Plugins menu, Stack Focuser. Drag and drop the stack_focuser_.class in that plugins folder, quit ImageJ and start ImageJ again. A Finder window opens where ImageJ is located and thatx should contain at least three folders: plugins and macros. You find the ImageJ Plugins folder if, when ImageJ is running, you right-click ImageJ in your Dock, then do ‘Options > Show in Finder’. Now you need to move the class file to the ImageJ Plugins folder. This is as simple as pressing the link above, which shows you the link Stack_Focuser_.class, clicking the link will bring the class file to your Downloads folder. Why did you not try the plugin? It is not that difficult, not even for a non-geek:ĭownload the Stack Focuser. Hi projecting the stack won’t give you a sharp image. If you need more help on the plugin, you best post the four sample images of the algae to allow us to follow your steps when you try out the afore mentioned plugin. It calculates per image (stack slice) groups of pixels that are sharp and then combines from each slice the sharpest areas to get the complete focused image. The plugin I linked to above seems to be exactly that, as inferred from its description. Sharp images have high contrast, neighbouring pixels can have wildly fluctuating values.Īs you want separate areas of all stack images to be combined into one image with extended depth of field, you best use readily available software. Out of focus images look blurred, all neighbouring picture elements all more or less have the same value. Technically, you want to grab the image area with the highest local change. You want to single out the focused part of each Z-plane, disregarding the rest and of all z-planes combine the sharpest areas into one single image. > and < keys on the keyboard forward and revers one frame.Ī stack can also be seen as a bunch of images on top of one another, each representing a Z-plane, or an image taken at a certain focal height with limited depth of field. Pressing the (now pause) button will stop the film. This stack can be regarded a film strip, and pressing the play button will show all images in succession, in an endless loop. Hi import the image sequence and thus create a stack, if I understand you correctly.
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