You may change the image type (here, bmp) according to your needs; just select the folder containing the images to process; the single RGB-channels are saved as greyscale.
"tilesrowcolumn=4" will produce 4x4=16 tiles from the original image; just select the folder containing the images to process; "filetype" specifies the images to process
[addnoise=how often noise is added; noisestandarddev=standard deviation of the noise added; imagesavestep=save (only) every n-th image; filetype specifies the images to process; just select the folder containing the images to process]
You may change the image type (here, bmp) according to your needs; just select the folder containing the images to process; the single RGB-channels are saved as greyscale.
The "Cyt/Nuc"-macro.
Here, you can download a package showing the function of the "Cyt/Nuc"-macro, that is able to quickly compare the amounts of a protein of interest in both cytosol and nucleus of immunostained cells or tissue samples.
Furthermore, the whole process of evaluation is documented in detail (recognized structures, results, used settings, date).
Download!
Just select the folder containing the original images to process; the single RGB-channels are saved as separate images in the according color with the correct name-extension.
Saves time to convert every single image manually using ZEN.
"filetype" specifies the images to process; you get a table (lower thresholds.txt) showing the lower thresholds for every single channel (red, green, blue) suggested by ImageJ; the upper threshold is always 255 for 8-bit or 4095 for 12-bit images.
For some reason it is NOT possible to name the directory that stores the single frames "frames"; if your video has more than 100,000 frames, add another if{save}-line.
This macro counts particles in all three channels of an RGB-image. The results are stored as data table and you get images for every single channel clearly showing the individual recognized particles - in order to check your settings, as well as to control and document the whole process of evaluation. Please download the "RGB-Counter"-package, it includes a very detailed manual, two different versions of the macro, and a few sample images to test it.
Here, you can download a package containing the macro, a manual and example images.
Download!
Sorting data is difficult when there are a variety of different parameters from each sample. "Ranker" places these samples in a ranking like athletes competing in different disciplines. This is useful if you want to identify the highest and lowest ranked samples.
Here, you can download a package containing the macro, a manual and example data.
Download!
A fast and well-described prime number generator for ImageJ
Here, you can download a package containing the macro and additional information.
Download!
MYOCYTER is a peer-reviewed ImageJ-macro (ScientificReports), that extracts more than 40 different parameters from high-speed videos of contracting cells/structures providing a incredible workflow. Please always use the latest version. Get the macro, sample videos and very detailed manuals here.
The update (v1.2) comes with many improvements: Better recognition, more functions, enhanced workflow!
Download the macro (v1.2) with manual and quickstart (14 MB).
NEW! Download the macro (v1.3) with manual and quickstart (16 MB). NEW!
PrimeLister (v1.1) generates about 250,000 primes/second in ImageJ and up to overwhelming 20 million primes/sec in C++.
Download the PrimeLister-codes for both ImageJ and C++, as well as the compiled EXEs right here: PrimeLister v1.1 Download
Here, you can find a video about the idea and the algorithm of PrimeLister:
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.
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. 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. 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. 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.
Get the publication here!
Visit our YouTube-Channel!
Visit our YouTube-Channel!