image-analysis-training-resources issueshttps://git.embl.de/grp-bio-it/image-analysis-training-resources/-/issues2019-07-27T07:18:08Zhttps://git.embl.de/grp-bio-it/image-analysis-training-resources/-/issues/22add python code examples2019-07-27T07:18:08ZChristian Tischeradd python code examplesalpha releasehttps://git.embl.de/grp-bio-it/image-analysis-training-resources/-/issues/23README needs updating2019-06-06T18:50:39ZToby HodgesREADME needs updatingOnce you/we have settled on a structure for the repository, it would be good to have that reflected in the README*, so that others can orientate themselves relatively quickly if they want to contribute.
* or maybe this makes more sense ...Once you/we have settled on a structure for the repository, it would be good to have that reflected in the README*, so that others can orientate themselves relatively quickly if they want to contribute.
* or maybe this makes more sense in `CONTRIBUTING.md`...https://git.embl.de/grp-bio-it/image-analysis-training-resources/-/issues/24web site landing page layout2019-07-24T13:56:34ZChristian Tischerweb site landing page layoutAny ideas how we could structure the top part where all the modules are shown a bit bit more?
Or you think it's fine like this? Looks actually fun, but it maybe it TMI.
https://grp-bio-it.embl-community.io/image-analysis-training-resour...Any ideas how we could structure the top part where all the modules are shown a bit bit more?
Or you think it's fine like this? Looks actually fun, but it maybe it TMI.
https://grp-bio-it.embl-community.io/image-analysis-training-resources/modules/filter_difference_of_gaussian.htmlToby HodgesToby Hodgeshttps://git.embl.de/grp-bio-it/image-analysis-training-resources/-/issues/25modules about image filters pros and cons2020-04-23T14:29:21ZChristian Tischermodules about image filters pros and cons@halavaty @hossain
It would be great to have a module that compares the pros and cons of popular filters, e.g., such as:
1. Gaussian Blur
1. Median Filter
Maybe we should restrict ourselves to maximally comparing three (**better only ...@halavaty @hossain
It would be great to have a module that compares the pros and cons of popular filters, e.g., such as:
1. Gaussian Blur
1. Median Filter
Maybe we should restrict ourselves to maximally comparing three (**better only two**) filters per module. To compare other filters we could make a new module. This would keep it nicely modular and at the same time not overload the students with information.M. Julius HossainM. Julius Hossainhttps://git.embl.de/grp-bio-it/image-analysis-training-resources/-/issues/26link to next module2019-06-07T06:49:16ZChristian Tischerlink to next moduleAt the bottom of each module I would like to have links to possible next modules.
How should this be done such that Mr. Jekyll understands?At the bottom of each module I would like to have links to possible next modules.
How should this be done such that Mr. Jekyll understands?Toby HodgesToby Hodgeshttps://git.embl.de/grp-bio-it/image-analysis-training-resources/-/issues/29Get a nicer URL2020-04-23T12:55:10ZToby HodgesGet a nicer URLThinking ahead. Once we've got a complete first set of material, we've setup better styling the website, and we've tried teaching with it for the first time, we might want to consider getting a shorter, cleaner URL for these pages.
Sugg...Thinking ahead. Once we've got a complete first set of material, we've setup better styling the website, and we've tried teaching with it for the first time, we might want to consider getting a shorter, cleaner URL for these pages.
Suggestions welcome in the comments...Toby HodgesToby Hodgeshttps://git.embl.de/grp-bio-it/image-analysis-training-resources/-/issues/39Pixel Data Type Conversion Exercises2020-04-23T14:28:36ZChristian TischerPixel Data Type Conversion Exercisesthe module about pixel data types needs some exercises.the module about pixel data types needs some exercises.https://git.embl.de/grp-bio-it/image-analysis-training-resources/-/issues/40image pixel size exercises2020-04-23T14:28:11ZChristian Tischerimage pixel size exercisesmaybe we should add an exercise where people should measure manually the distance between to voxels in an anisotropic image?maybe we should add an exercise where people should measure manually the distance between to voxels in an anisotropic image?https://git.embl.de/grp-bio-it/image-analysis-training-resources/-/issues/41anisotropic image rescaling2020-04-23T14:25:52ZChristian Tischeranisotropic image rescalingis it best practice to make an image isotropic by rescaling?
shall we teach that somewhere?is it best practice to make an image isotropic by rescaling?
shall we teach that somewhere?https://git.embl.de/grp-bio-it/image-analysis-training-resources/-/issues/43bio-it hackathon2019-07-12T09:55:58ZChristian Tischerbio-it hackathon@stamper
@halavaty
If people are motivated during the bio-it hackathon, the task could be to convert the current modules into the new style. It would be super helpful!
Example old style: https://git.embl.de/grp-bio-it/image-analysis-...@stamper
@halavaty
If people are motivated during the bio-it hackathon, the task could be to convert the current modules into the new style. It would be super helpful!
Example old style: https://git.embl.de/grp-bio-it/image-analysis-training-resources/raw/master/modules/filter_convolution.md
Example new style: https://git.embl.de/grp-bio-it/image-analysis-training-resources/raw/master/modules/binarization.mdToby HodgesToby Hodgeshttps://git.embl.de/grp-bio-it/image-analysis-training-resources/-/issues/48Need to add a list of contributors somewhere2019-07-24T13:56:34ZToby HodgesNeed to add a list of contributors somewherethis could be generated from the `_config.yml`, e.g.
```yml
contributors:
- Christian Tischer
- Toby Hodges
- Julius Hossain
- Aliaksandr Halavatyi
- Jean-Karim Hériché
- Constantin Pape
- Dominik Kutra
```
but it would ...this could be generated from the `_config.yml`, e.g.
```yml
contributors:
- Christian Tischer
- Toby Hodges
- Julius Hossain
- Aliaksandr Halavatyi
- Jean-Karim Hériché
- Constantin Pape
- Dominik Kutra
```
but it would be cool if we could find a way to use the GitLab/GitHub API to automate this...https://git.embl.de/grp-bio-it/image-analysis-training-resources/-/issues/54Meta-issue: New modules to be added2020-04-23T14:23:26ZToby HodgesMeta-issue: New modules to be added(feel free to add to this list if you think of more modules that could be added - but also create a separate Issue so that they can be referred to/closed as MRs for new modules are submitted & merged)
- [ ] General motivation (#35)
- [ ...(feel free to add to this list if you think of more modules that could be added - but also create a separate Issue so that they can be referred to/closed as MRs for new modules are submitted & merged)
- [ ] General motivation (#35)
- [ ] Hessians (#44)
- [ ] Image calibration? (#27)
- [ ] filter_neighbourhood; filter_rank; filter_morphological; local_background_subtraction (#18) (done already?)
- [ ] anisotropic image rescaling? (#41)alpha releasehttps://git.embl.de/grp-bio-it/image-analysis-training-resources/-/issues/55Concept maps need converting2020-04-23T14:22:58ZToby HodgesConcept maps need converting- [ ] [Convolution](https://grp-bio-it.embl-community.io/image-analysis-training-resources/filter_convolution/index.html)
- [ ] [Image math](https://grp-bio-it.embl-community.io/image-analysis-training-resources/filter_convolution/index....- [ ] [Convolution](https://grp-bio-it.embl-community.io/image-analysis-training-resources/filter_convolution/index.html)
- [ ] [Image math](https://grp-bio-it.embl-community.io/image-analysis-training-resources/filter_convolution/index.html)
- [ ] [Difference of Gaussian](https://grp-bio-it.embl-community.io/image-analysis-training-resources/filter_difference_of_gaussian/index.html)
- [ ] [Image display](https://grp-bio-it.embl-community.io/image-analysis-training-resources/image_display/index.html)
- [ ] [Intensity measurments](https://grp-bio-it.embl-community.io/image-analysis-training-resources/measure_intensities/index.html)
- [ ] [Object shape measurements](https://grp-bio-it.embl-community.io/image-analysis-training-resources/measure_shapes/index.html)
- [ ] [Object splitting](https://grp-bio-it.embl-community.io/image-analysis-training-resources/object_splitting/index.html)
- [ ] [Pixel data types](https://grp-bio-it.embl-community.io/image-analysis-training-resources/pixel_data_types/index.html)
- there are actually two maps on this page - ideally split into two separate modules
alpha releasehttps://git.embl.de/grp-bio-it/image-analysis-training-resources/-/issues/58Test concept map before building page2020-04-23T14:27:25ZToby HodgesTest concept map before building pageIs it possible to test whether a concept map has been correctly specified with Mermaid.js before the page is built/published? Debugging these concept maps isn't particularly easy...Is it possible to test whether a concept map has been correctly specified with Mermaid.js before the page is built/published? Debugging these concept maps isn't particularly easy...