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	Amplitude_2D	Background	Background_2D	X	Y	Z	X_2D	Y_2D	FWHM_X	FWHM_Y	FWHM_Z	FWHM_X_2D	FWHM_Y_2D	PrincipalAxis_1	PrincipalAxis_2	PrincipalAxis_3	PrincipalAxis_1_2D	PrincipalAxis_2_2D	SignalToBG	SignalToBG_2D	XYpixelsize	Zspacing	cov_xx	cov_xy	cov_xz	cov_yy	cov_yz	cov_zz	cov_xx_2D	cov_xy_2D	cov_yy_2D	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	sde_peak_2D	sde_background_2D	sde_X_2D	sde_Y_2D	sde_cov_xx_2D	sde_cov_xy_2D	sde_cov_yy_2D	version	Objective_id	PSF_path
100x_1_conf488Virtex.tif	2022-03-03	Microscope	100	1.4	4969.668887708917	5337.819377008636	108.68118565810401	112.06260978398689	3304.2501743562757	3250.4033761925416	3065.7405670931444	3298.302439467146	3250.4113027135386	200.8139074557401	197.03885411472754	674.9482557309917	183.72294307475494	176.22103947242965	675.8518951846926	199.23103476771948	195.54256297143823	184.93322114936828	174.9505023717054	45.72703966759075	47.63247426860641	65.0	200.0	7272.305680278791	199.51201664296516	3544.234164883923	7001.454943429444	1986.6819006579824	82153.39409342635	6087.112657801992	213.67205054291261	5600.155281533672	4.505314027916024	0.020623059963186995	0.06914746933299017	0.06784783324982839	0.23241058486654181	11.794695129256654	8.185734859446441	28.322224373959276	11.355300093289646	27.596443942593737	133.24416529759324	4.505314027916024	0.020623059963186995	0.06914746933299017	0.06784783324982839	0.23241058486654181	11.794695129256654	8.185734859446441	0.2.2.dev0+g1cb747a.d20221017	obj_1	./100x_1_conf488Virtex.tif_Bead_X3304.3_Y3250.4_Z3065.7.png
100x_1_conf488Virtex.tif	2022-03-03	Microscope	100	1.4	6131.783156459655	7007.7128858909955	108.97903673830632	112.03049813071806	3283.1815179892947	3369.970476029713	3032.554247929097	3276.851481699453	3370.657390994046	210.4996203597178	197.86302004157108	689.3745507955736	190.91529553428666	174.67418701487333	689.6867779885374	209.54607959880923	197.78706972073468	190.9553524915874	174.63039550165533	56.265712562536564	62.55183189236865	65.0	200.0	7990.743418986118	71.21282284528938	2449.8383466578707	7060.148226446074	195.46702412069595	85702.80681598671	6573.035837695339	54.41831030118964	5502.271462869397	4.621842915212504	0.02204379426143539	0.060262260154465876	0.05664426296450384	0.19735347823753954	10.774935265711402	7.1611338777206415	25.058014334542662	9.520360761496262	23.451758416706767	115.56192359712198	4.621842915212504	0.02204379426143539	0.060262260154465876	0.05664426296450384	0.19735347823753954	10.774935265711402	7.1611338777206415	0.2.2.dev0+g1cb747a.d20221017	obj_1	./100x_1_conf488Virtex.tif_Bead_X3283.2_Y3370.0_Z3032.6.png
100x_1_conf488Virtex.tif	2022-03-03	Microscope	100	1.4	5619.498212394354	5796.371864919072	108.65622592515462	111.58266064326322	3091.108753635228	3279.722510310466	3076.2986816645853	3084.318731921503	3278.6653904046307	214.82526951473534	210.45093794302085	708.1707538388272	205.59236614714763	202.64724874262387	709.557918556187	211.60340602370195	209.0379608329753	206.12587984384623	202.10455239686695	51.718142835783915	51.946887011866814	65.0	200.0	8322.52833820903	217.27766177392047	4878.624412287828	7987.047795051033	2326.0083470459012	90439.99432189878	7622.519106230307	100.7865902930646	7405.697623587783	4.830591872545995	0.0241438047271005	0.07013922523759801	0.06871098346239177	0.23121554192278806	12.798834896781521	8.867905979672457	30.29851519735856	12.282968059322448	29.332165284940636	139.08589313352223	4.830591872545995	0.0241438047271005	0.07013922523759801	0.06871098346239177	0.23121554192278806	12.798834896781521	8.867905979672457	0.2.2.dev0+g1cb747a.d20221017	obj_1	./100x_1_conf488Virtex.tif_Bead_X3091.1_Y3279.7_Z3076.3.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.

5. Desktop Icon for Windows¶

Follow this thread by Robert Haase.

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.