Clean-up for the course

[tibuch]

• [x] Tool installation

  • [x] Ready
  • [x] Checked
  • [x] Checked

• [ ] Digital image basics

  • [x] Ready
  • [x] Checked
  • [x] Checked

• [x] Lookup tables

  • [x] Ready
  • [x] Checked
  • [x] Checked

• [x] Spatial image calibration

  • [x] Ready
  • [x] Checked
  • [x] Checked
  • [ ] https://github.com/NEUBIAS/training-resources/issues/554, https://github.com/NEUBIAS/training-resources/pull/555

• [x] Image data types

  • [x] Ready
  • [x] Checked
  • [x] Checked

• [ ] N-dimensional images

  • [x] Ready
  • [ ] Checking https://github.com/NEUBIAS/training-resources/pull/559
  • [ ] Checked

• [ ] Image projections

  • [x] Ready
  • [x] Checked
  • [ ] Checked

• [x] Segmentation

  • [x] Ready
  • [x] Checked
  • [x] Checked

• [x] Manual thresholding

  • [x] Ready
  • [x] Checked
  • [x] Checked

• [x] Automated thresholding

  • [x] Ready
  • [x] Checked
  • [x] Checked

• [x] Connected component labeling

  • [x] Ready
  • [x] Checked
  • [x] Checked

• [ ] Object shape measurements PR #556

  • [x] Ready
  • [ ] Checked
  • [ ] Checked

• [x] Workflow: Basic 2D object analysis

  • [x] Ready
  • [x] Checked
  • [x] Checked

• [ ] Image neighborhood filtering see issue #498

  • [x] Ready
  • [ ] Checked
  • [ ] Checked

• [ ] Median filter see Issue #510

  • [x] Ready
  • [ ] Checked
  • [ ] Checked

• [ ] Object intensity measurements

  • [x] Ready
  • [ ] Checked
  • [ ] Checked

• [ ] Local background subtraction #511

  • [x] Ready
  • [x] Checked
  • [x] Checked

• [ ] Morphological filters

  • [x] Ready
  • [x] Checked
  • [x] Checked

• [ ] Workflow: 2D noisy object segmentation and filtering #499 PR: #558

  • [x] Ready
  • [ ] Checked
  • [ ] Checked

[grinic]

Luca (trainer from EMBL BCN) went through some modules and sent me some suggestions. They are a few renaming of variables in the "object intensity measure" module. Is it ok if I make changes directly to master?

[manerotoni]

If you are changing some typos in the text you can go on and rename on the master. If you are changing the code, in particular renaming of variables, you should definitely try on a branch and run the code first.

[manerotoni]

If you refactor the activities you can add the link as shown here https://github.com/NEUBIAS/training-resources/issues/517 I used it now in lut.md, binarization.md as examples.