grey) image that has color ascribed to it via a âLook Up Tableâ or LUT (a.k.a. Images with color come in three different forms: pseudo-color, 24-bit RGB image, or color composite image.Ī pseudo-colored image has a single channel, (i.e. 3.1 Merging images to a color composite.3 Merging transmitted light and fluorescence images.2.1 Interleaved multi-channel experiments.QuickFigures/TestingQuickFigures/Testing/Test Scale Bars at master Can you make figures with smaller czi files? You can also check if you can make figures using my test images (link below). There is a small chance that something about your particular files other than the file size is causing the issue. I have not yet found a more convenient solution for very large files. You may open an image in FIJI, crop the image, save as tiff and have QuickFigures use the tiff. When adding a new set of very large images, QuickFigures should unfreeze after a several seconds, allow you to proceed and then display a warning about file size. When I try to load a new set of images in the same panel, it freezes.įrom the screenshot, it looks like your images are much larger than my own. I have replies for each of your questions below. At some point, I will add an option to refresh the insets less frequently for larger images. There should still be a time lag while you are drawing/dragging insets since QuickFigures tries to refresh the inset panels with every mouse movement (which works for ordinary images but is not ideal for very large ones). For example, if you have the scale factor set to 0.2 in this option and subsequently create inset panels that are set to scale 5 fold larger than the parent scale, the inset panels will be shown at full resolution (0.2*5=1) while the main panel will be a lower resolution image. I should be able to get it to display larger images but it may take some additional work to reduce the time lag it takes before appearing.Īlso, you explained that: We need to figure out a way to represent the entire scanned area in low resolution and the insets at the highest possible.įor this, you can set a scale factor for the large image such that a smaller version (lower resolution) of it will be displayed (Option should be under âFigurewill appear in the update site list In the next dialog window click **Manage Update Sites** Äfter a moment, Fiji will tell you that you are up to date Äpply changes to make sure your Fiji is up to date Go the Help menu and select **'Update'** # Step 1: update Fiji (if not already up to date) Please reach out to me if you have any questions or recommendations. In order to save time and streamline the process I have created a toolset and ImageJ Plugin called QuickFigures. ![]() ![]() Assembling and editing these figures with even spacing, consistent font, text position, accurate scale bars and other features can be tedious and time consuming. Similar layouts of panels are used when displaying photographs, electron micrographs and other forms of images. Publications involving fluorescent microscopy generally contain many panels with split channels, merged images, scale bars and label text. grishkam/QuickFigures/blob/452565053dc38e12e3e3e81eca309f1624c04cdc/UserGuide/User Guide.md # QuickFigures User Guide The online user guide (also linked below) contains more details. Viewers may learn enough to start using QuickFigures in less than 10 minutes by watching the first video. The video playlist linked below demonstrates and explains the most useful features. QuickFigures can be used to create, align, and edit scientific figures with many panels, split channels, merged images, scale bars and label text. Thanks to the helpful suggestions from both reviewers and the ImageJ community, QuickFigures has been updated with new functions (details below). I created QuickFigures, a Fiji/ImageJ plugin for creating figures from microscopy images.
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