Measure Features

(c) 2016 - 2017 Barbara Piskur (Slovenian Forestry Insitute) and Janez Presern (Agricultural Institute of Slovenia)

This is simple Python3 tool to measure (electron) micrographs. The development was initiated after realisation that simple and simply extendable tool for work with rust (Pucciniales) electron micrographies is needed. Tool allows measuring of various qualities and quantities, like density and surface area on the image.

For example, as is it in the case of rusts (Pucciniales), density of thorns on the selected surface can be different from species to species. The tools assists with measuring and provides .csv with measurements and .pdf with picture where the estimations were taken from.

Dependencies

• Python >= 3.4
• Python packages
  • Matplotlib >= 2.0
  • Numpy >=1.11
  • Pandas >=19.2.

Open image file

Script opens image file through file dialog or startup parameters. If there is accompanying .txt file containing experimental metadata (at the moment only JEOL micrographs are supported), it tries to fetch the pixel size and scale bar size. Alternatively, image can be via startup parameters (below).

Startup parameters: --f ... opens file specified. Example: ./measure_features.py --f ./samples/Vzorec_120_005.tif

Open .csv file

Alternatively, one can open .csv file with old measurements. Image gets displayed automatically together with old "points-of-interest" drawn onto the image. User can either continue with his/her measurements or close old results untouched.

Measuring

Script offers measuring of two qualities, accessible via console interaction.

• Area measurement: Click on the edges of the area you would like to measure. Mark point in succession, ** do not jump back and forth**. Such selection can lead to misinterpretation what was the selected surface. Accept the measurements by pressing ENTER or middle mouse button. After area selection, there is possibility to count features (and density) inside the selected area. Density is computed and stored automatically. Units are square micrometers. Density unit is number of features per square micrometer.

• Length measurement: Click two points between which you would like to measure distance. After completition, user will be asked whether he/she wishes to continue with length measurements or quit length measurements. Units are square micrometers.

Saving results

A file dialog opens and prompts for the file name and location. Saving produces two files with the same name:

• .csv, which contains results, measurements and all other info required for restoring the measuring session (not implemented yet)
• .pdf, which contains image with measured regions, elements drawn in. .pdf is layered and can be further edit in varios vector manipulating software.

Warning: script overwrites existing files with the same name without prompt.

Acknowledgments

Development was supported by ARRS Z4-5518 (BP) and ARRS P4-0133 (JP).