The location and size of 1150 colonies are measured to quantify stitching accuracy. The datasets consist of three preparations of stem cell colonies seeded at low density and imaged with varying overlap (10 to 50%). We created 15 reference datasets to quantify MIST’s stitching accuracy. MIST has a performance-oriented implementation utilizing multicore hybrid CPU/GPU computing resources, which can process terabytes of time-lapse multi-channel mosaics 15 to 100 times faster than existing tools. MIST estimates the mechanical stage model parameters (actuator backlash, and stage repeatability ‘ r’) from computed pairwise translations and then minimizes stitching errors by optimizing the translations within a (4 r) 2 square area. We created MIST (Microscopy Image Stitching Tool) for rapid and accurate stitching of large 2D time-lapse mosaics. It also enables time-lapse studies of entire cell cultures in multiple imaging modalities. This can reduce sensor noise and remove sensor pixel errors (hot-pixels) in the final image.Automated microscopy can image specimens larger than the microscope’s field of view (FOV) by stitching overlapping image tiles. photos taken with closed shutter or lens cap on, are available, they are averaged and automatically subtracted from each input image. Here, the exposure of the stacked image is equal to the sum of the exposures of the individual input images.ĭark frame subtraction: When dark frames, i.e. Adding is particularly useful to synthetically generate longer exposed images from a set of individual images of the same scene. This can be used to reduce random noise from a set of photos of the same scene, thereby creating smoother images, particularly in image regions with low brightness and color variation.Īddition / Subtraction / Multiplication: Adds, subtracts or multiplies the images. Use this to remove star trails.Īverage: Averages the individual images. The length of the trails can be varied, of course.ĭarken: Compares the images and chooses the darker pixel at each location. See the corresponding gap filling tutorial.Ĭomet Mode: In ‘Lighten’ and ‘Gap Filling’ modes, StarStaX offers a ‘comet mode’ which adds a fading effect to the end of the star trails, simulating the look of comet trails. only the star trails) and control the amount of gap filling to be applied. The user can choose a threshold to limit processing to certain regions of the image (e.g. Gap Filling: Optimized ‘Lighten’ blending mode which tries to eliminate small gaps in star trails. In that case, the “Gap Filling” mode should be used, see below. If your camera pauses between consecutive exposures, there might be small gaps in the resulting star trails. Lighten: Compares the images and chooses the brightest pixel at each location. Mac: Time Lapse Assembler (freeware), ffmpeg or mencoder Use your favorite tool, to convert those images to a video, e.g.:.An image will be saved to the specified location after each image is processed.Select cumulative saving in “Blending” preferences tab.“Z” key for the all important 100% view.Double-click to center view on an image area (this area becomes the new “focus” for smooth zooming).Horizontal and vertical scrolling with mouse wheel or two-finger multi-touch gesture.Click and hold left mouse button to drag the image.
Plus (“+”) and minus (“-“) keys for smooth zooming.Load input images (menu bar or icon), optionally: load dark frames.Here is a quick overview of general usage: Just hover the mouse pointer over user interface elements of StarStaX to get a quick explanation of the underlying features and options. There are tooltips available for most of the options and features of StarStaX. To get started quickly, take a look at this tutorial and the help browser included in StarStaX. StarStaX has been designed to be easy-to-use without a steep learning curve.