Bio-IT issueshttps://git.embl.de/groups/grp-bio-it/-/issues2019-07-04T10:26:27Zhttps://git.embl.de/grp-bio-it/image-analysis-training-resources/-/issues/45make default platform configurable2019-07-04T10:26:27ZToby Hodgesmake default platform configurableFor the material to be adaptable to individual settings/workshops, it would be great to be able to configure a default platform for activities/exercises to be displayed in when a module loads. This would allow people to fork/import this ...For the material to be adaptable to individual settings/workshops, it would be great to be able to configure a default platform for activities/exercises to be displayed in when a module loads. This would allow people to fork/import this repo and set the default to whatever suits their puposes.Toby HodgesToby Hodgeshttps://git.embl.de/grp-bio-it/image-analysis-training-resources/-/issues/47Make activities consistent across platforms2020-04-23T14:26:24ZConstantin PapeMake activities consistent across platformsIt would be helpful to keep the activities more consistent between platforms (programming languages). This would help when following this resources as a standalone course, so
that the similarities / differences between the platforms are ...It would be helpful to keep the activities more consistent between platforms (programming languages). This would help when following this resources as a standalone course, so
that the similarities / differences between the platforms are more clear.
In the current binarization example, all platforms do something else:
- `imagejmacro`: binarize the image with threshold 30
- `jython`: binarize the image with threshold 60; the image is not read from file
- `matlab`: binarize the image with threshold that is an argument to the script
If there is a reason to have something not consistent, there should at least be some comment explaining it.
cc @tischer @stamperalpha releasehttps://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/50validate `_config.yml` before build2020-04-23T14:12:29ZToby Hodgesvalidate `_config.yml` before buildNow that the default platform is configurable, we should be validating the config file before pages get built.
A python script that parses the YAML and checks the values given should suffice...Now that the default platform is configurable, we should be validating the config file before pages get built.
A python script that parses the YAML and checks the values given should suffice...Toby HodgesToby Hodgeshttps://git.embl.de/grp-bio-it/image-analysis-training-resources/-/issues/52Rendering of lists in Exercises2020-04-23T12:52:42ZChristian TischerRendering of lists in Exercises@stamper
Currently, lists are not properly rendered within the `exercise_preface:`.
For example:
![image](/uploads/4da416f485d9ebe9216283e98eac8aad/image.png)@stamper
Currently, lists are not properly rendered within the `exercise_preface:`.
For example:
![image](/uploads/4da416f485d9ebe9216283e98eac8aad/image.png)alpha releaseToby HodgesToby Hodgeshttps://git.embl.de/grp-bio-it/image-analysis-training-resources/-/issues/53Converting modules to the new Style2020-04-23T14:22:30ZAliaksandr HalavatyiConverting modules to the new Style@tischer @hossain Please document module conversion in this table
| Module | Person | Done |
|-------------------------|-------------------------|-------------------------|
| Connecte...@tischer @hossain Please document module conversion in this table
| Module | Person | Done |
|-------------------------|-------------------------|-------------------------|
| Connected components | Tischi | yes |
| Image Pixels | Tischi | |
| Neighbourhood filters | Alex | yes |
| Morphological filters | | |
| Rank filters | Alex | |
| Pixel data type | Julius | |alpha releasehttps://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/56clean up template folders2019-07-24T13:56:34ZToby Hodgesclean up template foldersWe should be able to remove the Carpentries-related images etc to reduce the size of the repoWe should be able to remove the Carpentries-related images etc to reduce the size of the repoToby HodgesToby Hodgeshttps://git.embl.de/grp-bio-it/image-analysis-training-resources/-/issues/57Conditional layout for map & example diagram2020-04-23T14:27:52ZToby HodgesConditional layout for map & example diagramAdd some conditional layout to center-align the concept map if an example figure is not included.Add some conditional layout to center-align the concept map if an example figure is not included.Toby HodgesToby Hodgeshttps://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...https://git.embl.de/grp-bio-it/image-analysis-training-resources/-/issues/60JS snippet showing up where it shouldn't2019-07-26T09:29:19ZToby HodgesJS snippet showing up where it shouldn'tWhen there are no platform-specific activities or exercises for a module, some of the JS code that changes the visibility of blocks based on the chosen platform becomes visible at the top of the page.
![stray_JS](/uploads/9aed8e4c940f5...When there are no platform-specific activities or exercises for a module, some of the JS code that changes the visibility of blocks based on the chosen platform becomes visible at the top of the page.
![stray_JS](/uploads/9aed8e4c940f523ec7194dd3ee63e3f9/stray_JS.png)Toby HodgesToby Hodgeshttps://git.embl.de/grp-bio-it/image-analysis-training-resources/-/issues/61Activities shown without explicitly selecting one2019-07-26T09:29:19Z Stefan HelfrichActivities shown without explicitly selecting oneIn particular in the _Connected components_ and _Neighbourhood image filters_ modules, the activity is already shown when the page is opened. This issue remains when an additional activity is added (so it's not due to only a single activ...In particular in the _Connected components_ and _Neighbourhood image filters_ modules, the activity is already shown when the page is opened. This issue remains when an additional activity is added (so it's not due to only a single activity being available).Toby HodgesToby Hodgeshttps://git.embl.de/grp-bio-it/image-analysis-training-resources/-/issues/62README needs updating again2020-04-23T12:51:16ZToby HodgesREADME needs updating againThe description of the repository structure is outdated since we switched to the adapted Carpentries style.The description of the repository structure is outdated since we switched to the adapted Carpentries style.alpha releaseToby HodgesToby Hodgeshttps://git.embl.de/grp-bio-it/grassroots/-/issues/6Code of Conduct2021-10-19T15:23:03ZLisanna PaladinCode of ConductCreate Code of Conduct.
It should include links/quotes from the relevant documents at EMBL:
- [EMBL Conference and Courses CoC](https://www.embl.de/training/events/info_participants/codeofconduct/#:~:text=EMBL%20is%20dedicated%20to%20pr...Create Code of Conduct.
It should include links/quotes from the relevant documents at EMBL:
- [EMBL Conference and Courses CoC](https://www.embl.de/training/events/info_participants/codeofconduct/#:~:text=EMBL%20is%20dedicated%20to%20providing,thereof)%20or%20manner%20of%20articulation.)
- [Magna Carta for researchers](http://www.embl-hamburg.de/aboutus/communication_outreach/media_relations/2006/061214_brussels/)
- [How to deal with
problems at EMBL](https://www.embl.org/documents/wp-content/uploads/2020/07/brochure_how-to-deal-with-problems.pdf)OLS-4 Week 5