image-analysis-training-resources issueshttps://git.embl.de/grp-bio-it/image-analysis-training-resources/-/issues2020-04-23T14:26:24Zhttps://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/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/20Concept Maps not rendering in Chrome2019-06-06T18:51:59ZToby HodgesConcept Maps not rendering in ChromeSee https://grp-bio-it.embl-community.io/image-analysis-training-resources/modules/binarization.html as an example. Looks like this is because Chrome doesn't like some characters in the specification of the map visualisation.See https://grp-bio-it.embl-community.io/image-analysis-training-resources/modules/binarization.html as an example. Looks like this is because Chrome doesn't like some characters in the specification of the map visualisation.https://git.embl.de/grp-bio-it/image-analysis-training-resources/-/issues/15add content to `index.md`2019-06-06T19:00:01ZToby Hodgesadd content to `index.md`The `index.md` file is currently only a placeholder. As the landing page for the site, it should be a bit more detailed and helpful.The `index.md` file is currently only a placeholder. As the landing page for the site, it should be a bit more detailed and helpful.https://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/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/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/59Workshop for image data quality control2019-07-24T09:51:00ZChristian TischerWorkshop for image data quality controlIt would be good to combine modules into a workshop that focusses on image data handling and quality control.
The point is to be able to judge whether an image acquired on a microscope is of sufficient quality.It would be good to combine modules into a workshop that focusses on image data handling and quality control.
The point is to be able to judge whether an image acquired on a microscope is of sufficient quality.Christian TischerChristian Tischerhttps://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/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/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/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/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/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/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/51Figures2019-07-18T07:31:56ZChristian TischerFigures@pape @halavaty @stamper @hossain
I made a Google Slides document for figures:
https://docs.google.com/presentation/d/1ZEzX8YrsCq6sAW6T5hEUkM7RYOyVNfpiafSo-b9VC3U/edit?usp=sharing@pape @halavaty @stamper @hossain
I made a Google Slides document for figures:
https://docs.google.com/presentation/d/1ZEzX8YrsCq6sAW6T5hEUkM7RYOyVNfpiafSo-b9VC3U/edit?usp=sharinghttps://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/49Unification of used images in trainig material2019-07-04T13:11:11ZDominik KutraUnification of used images in trainig material@stamper @pape and me have been working a bit on the Python training material during the first Annual Bio-IT Hackathon.
One of the outcomes is a re-organization of the already existing [Python training material](https://git.embl.de/grp-...@stamper @pape and me have been working a bit on the Python training material during the first Annual Bio-IT Hackathon.
One of the outcomes is a re-organization of the already existing [Python training material](https://git.embl.de/grp-bio-it/image-analysis-with-python/). Previously, it was one long Jupyter Notebook. We want to break it up into more digestible bits. The idea is then to link to static/interactive notebooks from the relevant "activity" section if python is chosen.
It is already very nice that all teaching material (I mean the language agnostic parts that only work with concepts) in this repo follows the same structure.
I know that one of the ideas of this repo is to provide a set of example images that are free to use for everyone. This is great of course. I just want to make a point for not using different images in the example teaching materials.
The benefit I see for users is that they don't get distracted by peculiarities of new images in every concept they have to grasp.
It could still be part of exercises to apply concepts to different images to better understand the effects.
What are your opinions on using the same image (or set of images) in all teaching examples?
Related:
* [issue tracking restructuring of Python teaching material](https://git.embl.de/grp-bio-it/image-analysis-with-python/issues/6)https://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/46Jupyter notebooks for Python2019-07-04T08:05:01ZDominik KutraJupyter notebooks for PythonIn the context of python courses it would be great to refer to Jupyter examples
**Plan**:
* Create new repo with Jypyter notebooks, modeled after the concept maps
* Link to repo with example Jupyter Notebooks
* Binder for interactive s...In the context of python courses it would be great to refer to Jupyter examples
**Plan**:
* Create new repo with Jypyter notebooks, modeled after the concept maps
* Link to repo with example Jupyter Notebooks
* Binder for interactive session
* Also have code examples after selecting Python in drop-down