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NoiSee

682 bytes added, 06:44, 31 March 2018
Update installation and usage instructions for beads method
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{{Infobox
| software = ImageJ
'''NoiSee''' - An easy-to-use ImageJ macro for measuring SNR (signal-to-noise ratio) of light microscopes.
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= Installation =
 
[[Following_an_update_site|Enable the NoiSee update site]] and restart Fiji.
 
= Usage =
 
NoiSee consists of two independent macros, one for each type of analysis:
 
* The '''Beads Method''' for a time-lapse acquisition of fluorescent beads. NOTE: this method will '''NOT''' work for sub-resolution beads! The beads should have a diameter of at least '''ten''' pixels in the acquired image.
== Installation ==* The '''Fluorescein Method''' for an acquisition of a fluorescent solution and a dark field (i.e. "''laser off''") image, both single frame (no Z-stack, no time-lapse).
Enable the corresponding update site and restart Fiji.== Bead Method ==
== Usage ==Type "''NoiSee''" in the quick search bar, select "''Bead Analysis''" and click "''Run''". Otherwise, you can also locate the NoiSee macros in the Plugins > NoiSee menu.
=== Bead Method ===First, the parameters dialog will appear with the following input fields / options:
* Start Fiji* Type “NoiSee” in the quick search bar, select “Bead Analysis” and click “Run”* In the parameters dialog** Specify image field specify the path to the a time lapse bead beads imagestored in a format readable by [[Bio-Formats]].*** All result files generated by NoiSee will be placed in a new sub-folder located in the same directory as the input image.** Specify the The approximate beads diameter of the beads has to be specified in pixels. NoiSee uses the “Find Maxima” "''Find Maxima''" function to automatically detect beads above a certain intensity threshold that needs to be roughly estimated. Starting values for this estimate depending on the detector type used, e.g. 50 for PMTs, 10 for Hybrid detectors in photon counting mode or 500 for camera based systems.*** If not all beads are identified the estimate should be lower.*** If peaks other than beads are identified the estimate should be higher.** ''Note: While NoiSee tries to exclude hot pixels and overexposed beads, these would ideally be already avoided during imaging.''** Choose whether you wish to create kymographs. We recommend to do so as they are useful to inspect sample drift and bleaching.** NoiSee can further save additional data (individual measurements per bead) as txt-files.** All images and plots created by NoiSee can optionally be saved in a PDF report.** ROIs used for measurements are available from the ROI manger and can additionally be visualized as extra images.** Press “OK” "''OK''" and wait for NoiSee to finish its calculations.** A summary of all NoiSee results is automatically saved as a txt-file.
== Example ==
== Citation ==
Please note that NoiSee is based on a publication. If you use it for related
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