Photon Transfer Curve Assistant
Utility to help establish camera and illumination properties.
This plugin will take series of images with varying exposure times, and present you with the mean and standard deviation image obtained at each exposure.
Provide even, continuous illumination of your camera. It may be helpful
to set an ROI in the center of the field of view so that illumination
is more homogenuous.
Establish thelowest exposure time possible with your camera, and establish the
exposure time that just leads to saturation of your image (which will
depend on illumination intensity). Decide how many exposures (i.e.,
different exposure times) you would like to obtain, and how many frames
per exposure. The Spacing exponent parameter determines the spacing of
exposure times. A vlaue of 1.0 leads to a linear series, the default 0.5
should give you more higher exposures, which may help the analysis.
The plugin will then ask you to close the shutter, or prevent light of reaching the sensor in any other way possible so that it can obtain a true dark image.
After the plugin collected dark images, it will ask you to switch the light back on.
After all images are collected (which may take a while), an ImageJ stack with two channels, one the mean, the other channel the std.dev. at each exposure will be shown. These images shoudl be especially informative for sCMOS cameras, where the per pixel variation in noise can be very high.
Also show is an ImageJ Results tables. This has the following columns:
- Exposure: Exposure time used to acquire the Stacks of Images
- Average mean Intensity of the images in the stack.
- Noise: Average Std. Deviation of the images in the stack.
- Read+Shot Noise: Each image in the stack was subtracted from the first image, then the Standard Deviation was calculated and divided by the Sqrt of 2. This procedure will subtract the Fixed Pattern Noise in the image, so only Read Noise and Shot Noise is remaining.
- Std. Dev.: Variation in mean intensity of the images. If this number is high, most likely the light source is fluctuating.
- ADU Estimate: Mean Intenisty divided by variance.
- Local Slope: When close to 0.5, this image is shot noise limited and the ADU should be valid.
The plugin will also plot the data on a log log plot, fit a line and calculate the ADU (Photon Conversion Factor, electrons/DN), and express the read noise in electrond.
You can experiment with the plugin with the Demo Camera. To do so, set the “Mode” property to “Noise”. You can change the “Photon Flux” (the simulated brightness of the light source), to the highest value possible so that it does not take too long to acquire data. Set the ReadNoise (electrons) to 25, and run the plugin to get the results shown here (Minimum 0.001, Max 16ms, Nr. Exposures 16, Nr Frames 25, Spacing 0.5).
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