![]() To take care of these 'gaps' in the nuclei mask we are going to use the Fill Holes option found under Process -> Binary -> Fill Holes. You can see below that we have some small speckled areas detected outside the nuclei, as well as some spots within the nuclei that are not masked completely. In this image mask there are a few blemishes that may affect the measurement. If you are working with a mask you can perfect your selection using filters. Which is why we often create a mask instead. If you choose to work with the threshold you can skip straight to measurements from here, however the threshold is not always a perfect selection of the data. For your own data you will need to find a threshold that works for you.Ĭlose the options box to keep the selection as a threshold, or click Apply to generate mask as previously described. Here I have used the Default algorithm set at 65 and 255. Then go to Image -> Adjust -> Threshold (or use short cut Ctl + Shift + T).įit your threshold to the data as best as possible. This image is already grey, but apply a grey LUT if you are working with a colour image and duplicate the image if you would like. You may also like to Duplicate the original image and work on a copy. Check that the scale is calibrated before carrying out any further steps.įor colour images I like to apply a grey LUT to allow better contrast between the stain and background during thresholding. In this example we will use a threshold, but you can also select a specific area to measure by using an ROI. Without a selection, the program would give an area measurement for the entire image, rather than just the area of interest. We also need to select an area within the image that we want to measure. Checking and setting the scale calibration was covered in FIJI Basics. To perform any measurements on our image we must ensure the scale is calibrated. In this section we use the images RGB-blue.tif, RGB-green.tif, NeuralTubeRed.tif and Nuclei-1.tif for demonstration. ![]() Here, our instructions become more speicified as wel go through several examples of common measurements using the different tools in FIJI. Due to the open source code and the expandable setup, the MyoPulser can be easily adapted to even highly specific requirements and together with the software MYOCYTER it represents a complete cardiomyophysiological measuring station.Many of the simple FIJI functions that you have previously learnt about can be combined with other tools for more complex processes to analyse and measure your data. Electrostimulation of isolated B6 cardiomyocytes showed very little deviation of the observed cellular contraction from the applied pulse settings of the device, while the carbon electrodes used proved to be biologically inert in long-term experiments. The device enables the user to select between different pulse types (monophasic, alternating, bi- and polyphasic) adjust the length of an applied pulse (1–200 ms), the gap between two consecutive pulses (20–2000 ms), application of irregular pulses with random length and gaps (simulation of arrhythmia) in a user-defined range, as well as manual pulsing, while extensive data are recorded for every single pulse during the experiment. In this work, construction, functions and application of the MyoPulser are explained in detail, the electronic pacemaker is also tested on isolated cardiomyocytes and HT22-cells to quantify biological effects of pacing. After providing the free software MYOCYTER that analyzes a large amount of data from videos of contracting cells, tissues or organs, we now present an “Arduino”-based programmable, customizable and cost-effective electronic pacemaker (“ MyoPulser”) that triggers contraction by electric stimulation of the sample at arbitrary frequencies. ![]()
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