/musurf-reader

Functions for importing µsurf confocal microscope binary file formats

Primary LanguagePythonMIT LicenseMIT

musurf-reader

Functions for importing µsurf confocal microscope binary file formats

µsurf File Formats

Type Function
.orginal Contains measurement properties as well as height and intensity data. Subimages were stitched to a whole image.
.nms Same structure as .orginal, but contains the data changed by the µsoft software (filtering, fitting, ...). Same content as .orginal when no post-processing took place.
.sms Contains a list of the measurement's subimages, each containing height and intensity information.
.smt Same content as .sms file, but signals the microscope µsoft software to stitch the subimages on file import.
.smi Contains image stitching information
.txt Human-readable height data as ASCII table

Supported File Features

Support for OM_MS_2.0 file versions only.

Type Supported Features
.orginal
.nms
x and y coordinates, height and intensity data
.sms
.smt
x and y coordinates, height and intensity data for each individual image
.smi (experimental) image count in x and y direction as well as the image overlap parameter
.txt x and y coordinates and height data

Usage

Function names consist of read + file extension

Example:

import musurf_reader as mur

# load whole measurement
x, y, image, intensity = mur.readnms("D:\Measurement.nms")

# or load individual images in a measurement
x, y, images, intensities = mur.readsms("D:\Measurement.sms")

Required Packages

numpy, struct

Tested with Python 3.8 and PyCharm 2020.3.2