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pyme-psf-extraction

A bead PSF extraction recipe module written for PYME.

Designed to crop, align and average bead PSFs. Some capability for rejecting bad bead PSFs are provided. Deconvolution not part of this module but is available in PYME.

System requirements

  • Windows, Linux or OS X
  • Python 2.7
  • PYME (>18.7.18) and dependencies
  • Tested on Windows 10 with PYME (18.7.18)

Installation

  1. Clone repository.
  2. Run the following in the project folder. 
    	python setup.py develop
  3. Start dh5view (PYME).

(Runtime < 5 min)

Demo

  1. Open this simulated image of beads (beads_simulated.h5) with dh5view (PYME).
  2. Load and run this demo recipe (bead_psf_extraction.yaml).
  3. Open the extracted PSF by clicking the output (default: psf_combined) on the final AveragePSF module.

(Runtime < 5 min)

Instructions

  1. Refer to PYME documention for general use of PYME.

  2. Open image file with dh5view (PYME).

  3. Chain the modules in this order:

    1. CombineBeadStacks (optional)
    2. Cleanup
    3. DetectPSF
    4. CropPSF
    5. AlignPSF
    6. AveragePSF

    Detailed description of each module and their inputs, outputs and parameters are accessible in PYME.

  4. Run recipe.

  5. Click on the extracted PSF output from AveragePSF and save as necessary.

To do's

  • Change some of the parameters from pixel size to nanometer
  • Add more metadata