Download
All platforms: ImageJ plugin
If you only want the plugin or are using an operating system other than Windows, download following package:
This download contains only the plugin and dependency libraries. Please do not forget to obtain compiled MISA++ packages for your operating system that are interfaced with the plugin.
Linux
We provide ready-to-install packages for Ubuntu 18.04 and Ubuntu 19.10 that contains following components:
- MISA++ core components (MISA++ Core, MISA++ Analyzer)
- Example implementations of third-party library integrations (OpenCV, OME TIFF)
- Example implementations of image analysis algorithms (Tissue segmentation, Kidney glomeruli segmenation, OME visualizer, and more)
- ImageJ plugin binaries, including dependency libraries
You can install the *.deb packages using sudo apt install ./*.deb. Put the plugin files (located in the misa-imagej folder)
into an existing Fiji installation to install the ImageJ plugin.
Windows
We provide a ready-to-use Fiji distribution that comes pre-installed with MISA++ for ImageJ, MISA++ Kidney Glomeruli Segmentation, MISA++ Tissue Segmentation, MISA++ OME Visualizer, MISA++ Microbenchmarks, MISA++ Deconvolution Simulation, MISA++ Cell Segmentation and MISA++ Result Analyzer.
Alternatively, you can download only the MISA++ binaries.
MISA++ is developed on Linux - We consider this Windows release as experimental. We are aware of a bug that causes freezes of multi-threaded MISA++ workloads if executed from within ImageJ. As workaround, export MISA++ runs as standalone package and run MISA++ via the command line interface.
Please make sure that your anti virus protection does not block the MISA++ application. Try refreshing the list of modules if a module could not be loaded.
Source code
The software is Open Source and licensed under BSD-2-Clause. You can find the source codes of the MISA++ framework, modules and applications under following links:
| Library | Source code | Class reference |
|---|---|---|
| MISA++ Core | Download source code | Open |
| MISA++ Imaging | Download source code | Open |
| MISA++ Microbenchmarks | Download source code | |
| MISA++ Deconvolution Simulation | Download source code | |
| MISA++ Cell Segmentation | Download source code | |
| MISA++ OME | Download source code | Open |
| MISA++ OME Visualizer | Download source code | Open |
| MISA++ Tissue Segmentation | Download source code | Open |
| MISA++ Kidney Glomeruli Segmentation | Download source code | Open |
| MISA++ Result Analyzer | Download source code | Open |
| MISA++ for ImageJ | Download source code |
git clone https://github.com/applied-systems-biology/misaxx-core.git
git clone https://github.com/applied-systems-biology/misaxx-imaging.git
git clone https://github.com/applied-systems-biology/misaxx-microbench.git
git clone https://github.com/applied-systems-biology/misaxx-deconvolve.git
git clone https://github.com/applied-systems-biology/misaxx-segment-cells.git
git clone https://github.com/applied-systems-biology/misaxx-ome.git
git clone https://github.com/applied-systems-biology/misaxx-ome-visualizer.git
git clone https://github.com/applied-systems-biology/misaxx-tissue.git
git clone https://github.com/applied-systems-biology/misaxx-kidney-glomeruli.git
git clone https://github.com/applied-systems-biology/misaxx-analyzer.git
git clone https://github.com/applied-systems-biology/misa-imagej.git
Linux docker builds
We use automated build scripts to compile Linux packages. These scripts use a Docker environment and can be found here.
Windows Cygwin builds (experimental)
To build MISA++ on Windows, we use the Cygwin environment. Our script can be found here.
Logos
Download following package for the MISA++ logos:
Example data
Our step by step guide requires you to download example data:
The example data was published by Klingberg et. al
Klingberg, Anika, et al. “Fully automated evaluation of total glomerular number and capillary tuft size in nephritic kidneys using lightsheet microscopy.” Journal of the American Society of Nephrology 28.2 (2017): 452-459.
Other example data
If you want to try out other algorithms (as well as Python and Java implementations), you can find appropriate example data here:
| Algorithm | Download |
|---|---|
| Glomeruli segmentation (MISA++) | Download example data |
| Glomeruli segmentation (Python, Java) | Download example data |
| Cell segmentation (MISA++) | Download example data |
| Cell segmentation (Python, Java) | Download example data |
| Deconvolution | Download example data |
| Single operation benchamrks | Download example data |
Publication supplements
In our publication, we compare MISA++ against Java and Python implementations. You can find the compiled Java binaries here. All source codes are available in our all-in-one code repository.