SIMcheck is a package of ImageJ tools for assessing the quality and reliability of Structured Illumination Microscopy (SIM) data.
Copyright Graeme Ball and Lothar Schermelleh, Micron Oxford, Department of Biochemistry, University of Oxford. License GPL unless stated otherwise in a given file (in particular, SIMcheck uses modified versions of ImageJ's Slicer plugin and Paul Baggethun's Radial Profile Plot plugin).
The simplest way to install SIMcheck and keep it up to date on your system is using the ImageJ updater. SIMcheck is available via an ImageJ update site so you only need to activate it from the list of sites. See "How to follow an update site" for more details
If for some reason the ImageJ updater is not available, the jar file for the latest release can still be downloaded manually from the update site. If so, the file extension needs to be manually adjusted adn dependencies will need to be installed somehow.
The project uses the maven build and dependency management tool, so to
build it, run the following command (.jar file appears in target/
):
mvn package
In addition, SIMcheck is also released via Sonatype to ease its use by other projects:
<dependency>
<groupId>uk.ac.ox.micron</groupId>
<artifactId>SIMcheck</artifactId>
<version></version>
</dependency>
Check | Statistic(s) | Comments
-------------------- | ----------------------------------- | ------------------ Intensity Profiles | bleaching, flicker, angle intensity | Motion / Illum Var | None: angle differences colored | Fourier Projections | None: check pattern / spots OK | Modulation Contrast | feature MCNR acceptable? | Wiener estimate
Check | Statistic(s) | Comments
-------------------- | ----------------------------------- | ------------------ Intensity Histogram | +ve/-ve ratio acceptable? | top/bottom 0.01% SA Mismatch | stdDev of miniumum vs. mean | shows OTF mismatch Fourier Plots | None: symmetry+profile OK? | Mod Contrast Map | None: inspect MCNR of features | green=saturated
Check | Statistic(s) | Comments
-------------------- | ----------------------------------- | ------------------ Illum. Phase Steps | phase step & range stable? | +k0, linespacing Pattern Focus | None: check for "zipper" pattern |
SIMcheck_.jar
file1.2: post-release updates, bugfixes & refactoring
1.3: PSF and OTF symmetry, extent, shape & order separation
1.4: additional numerical stats, including resolution estimate
1.5: ImageJ2 reimplementation / headless running
1.6: check name updates & test suite
2.0: integrated swing GUI control
(Kai Wicker)
Camera background: subtraction
optical distortions & uneven gain: flat-field correction
illumination intensity fluctuations: normalisation (after background subtraction)
sample drift between images: drift correction by means of cross-correlation
unknown grating period: find grating vector using component cross-correlations
fluctuations in grating phase: optimization of mixing matrix
fluctuation of order strengths between images
sample drift between focal slices: drift correction through cross-correlation
unknown zero grating phase: global phase via cross-correlation
drift between rotational orientations: drift correction through cross-correlation
unknown order strengths: compare different separated components