napari-psf-analysis

This napari plugin was generated with Cookiecutter using @napari's cookiecutter-napari-plugin template.

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A plugin to analyse point spread funcitons (PSFs) of optical systems.

Usage

Starting Point

To run a PSF analysis open an image of acquired beads. Add a point-layer and indicate the beads you want to measure by adding a point.

Run Analyis

Open the plugin (Plugins > napari-psf-analysis > PSF Analysis) and ensure that your bead image and point layers are select in the Basic tab under Image and Points respectively. In the Advanced tab further information can be provided. Only the filled in fields of the Advanced tab are saved in the output.

After verifying all input fields click Extract PSFs.

Discard and Save Measurement

Once the PSF extraction has finished a new layer (Analyzed Beads) appears, holding a summary image for every selected bead. Individual summaries can be discarded by clicking the Delete Displayed Measurement button.

Results are saved to the selected Save Dir by clicking the Save Measurements button.

Note: Beads for which the bounding box does not fit within the image are automatically excluded from the analysis and no output is generated.

Saved Data

Every image of the Analyzed Beads layer is saved as {source_image_name}_X {bead-centroid-x}_Y{bead-centroid-y}_Z{bead-centroid-z}.png file. Additionally a PSFMeasurement_{source_image_acquisition_date}_ {source_image_name}_{microscope_name}_{magnification}_{NA}.csv file is stored containing the measured values and all filled in fields.

For the demo gif above the following table is saved:

ImageName	Date	Microscope	Magnification	NA	Amplitude	Background	X	Y	Z	FWHM_X	FWHM_Y	FWHM_Z	PrincipalAxis_1	PrincipalAxis_2	PrincipalAxis_3	SignalToBG	XYpixelsize	Zspacing	cov_xx	cov_xy	cov_xz	cov_yy	cov_yz	cov_zz	sde_peak	sde_background	sde_X	sde_Y	sde_Z	sde_cov_xx	sde_cov_xy	sde_cov_xz	sde_cov_yy	sde_cov_yz	sde_cov_zz	Comment	PSF_path
100x_1_conf488Virtex.tif	2022-03-03	Microscope	100	1.4	5169.285944782688	110.18242108419038	2605.150064016795	2778.5159415714847	2223.0135754293333	205.83948141718292	193.26935441526453	673.333737589546	673.8395142125338	204.76810910270055	192.64368202154003	46.91570482765882	65.0	200.0	7640.8541537792735	-13.739986414927806	2461.133326066555	6736.131301493249	-1761.0316747094355	81760.83213128973	6.07230627881135	0.0428908418118399	0.0918331172590858	0.08622431079805634	0.30039707647545805	16.058330709118493	10.658894965304015	37.31418836385325	14.157198228507017	34.96459026793594	171.82884173452643	This is a demo.	./100x_1_conf488Virtex.tif_Bead_X2605.2_Y2778.5_Z2223.0.png
100x_1_conf488Virtex.tif	2022-03-03	Microscope	100	1.4	6135.157449356215	110.45693133711426	2579.1750636343136	2665.971138363623	2236.556334604507	210.3414510686511	197.70468562397645	688.7450949822045	689.0569862986882	209.38893767869146	197.62898832950918	55.543435573379554	65.0	200.0	7978.739450747766	71.03860432658904	2445.186895806542	7048.853370163676	194.33624544039762	85546.37080807924	6.427131015205848	0.04702336845023734	0.08368900397680192	0.0786607859867236	0.2740328722683267	14.954667965040326	9.937027929319177	34.76778883464614	13.21218589548314	32.53756104188376	160.34176367808521	This is a demo.	./100x_1_conf488Virtex.tif_Bead_X2579.2_Y2666.0_Z2236.6.png
100x_1_conf488Virtex.tif	2022-03-03	Microscope	100	1.4	5622.117168996411	110.12846686628077	2387.1094900635194	2575.7229681487956	2280.3111520343996	214.6603075814513	210.29252188934618	707.5199298039764	708.9044265632655	211.44593966381632	208.88171792203815	51.05053515203157	65.0	200.0	8309.75169186637	216.78540934275736	4866.991328053463	7975.027887810296	2320.8118890686897	90273.83813806984	6.840381484837519	0.052450225692372655	0.09919251952617283	0.09717397041964153	0.32694856225371205	18.089302104598307	12.53155240411209	42.809428898592365	17.360668540008014	41.444943537461285	196.52752653343444	This is a demo.	./100x_1_conf488Virtex.tif_Bead_X2387.1_Y2575.7_Z2280.3.png

With the three summary images:

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Installation

We recommend installation into a fresh conda environment.

1. Install napari

conda create -y -n psf-analysis -c conda-forge python=3.9

conda activate psf-analysis

python -m pip install "napari[all]"

2. Install napari-aicsimageio and bioformats

Required if you want to open other files than .tif e.g. .stk. .

Note: See napari-aicsimageio for more information about opening images.

conda install -c conda-forge openjdk

conda deactivate
conda activate psf-analysis

python -m pip install "bfio[bioformats]"
python -m pip install "aicsimageio[all]"
python -m pip install napari-aicsimageio

3. Install napari-psf-analysis

You can install napari-psf-analysis via pip:

python -m pip install napari-psf-analysis

4. Optional Set Config

You can provide a config yaml file with the available microscope names and a default save directory. This will change the Microscope text field to a drop down menu and change the default save directory.

example_config.yaml

microscopes:
  - TIRF
  - Zeiss Z1
output_path: "D:\\psf_analysis\\measurements"

To use this config navigate to Plugins > napari-psf-analysis > Set Config and select the config file.

Note: The save path is OS specific.

Contributing

Contributions are very welcome. Tests can be run with tox, please ensure the coverage at least stays the same before you submit a pull request.

License

Distributed under the terms of the BSD-3 license, "napari-psf-analysis" is free and open source software

Issues

If you encounter any problems, please file an issue along with a detailed description.