image-analysis-training-resources merge requestshttps://git.embl.de/grp-bio-it/image-analysis-training-resources/-/merge_requests2021-10-21T15:43:51Zhttps://git.embl.de/grp-bio-it/image-analysis-training-resources/-/merge_requests/41Pixel data types julius2021-10-21T15:43:51ZM. Julius HossainPixel data types juliusChristian TischerChristian Tischerhttps://git.embl.de/grp-bio-it/image-analysis-training-resources/-/merge_requests/51Update pixels.md2021-10-21T15:43:38ZChristian TischerUpdate pixels.mdChristian TischerChristian Tischerhttps://git.embl.de/grp-bio-it/image-analysis-training-resources/-/merge_requests/49Convert Image Math module2020-04-23T14:33:38ZToby HodgesConvert Image Math moduleI've ported the "Image Math" module and changed the Gravizo concept map to Mermaid.js.
This module includes a lot of TODOs - please could someone take a look at it and add some more content (learning objectives and prerequisites at a mi...I've ported the "Image Math" module and changed the Gravizo concept map to Mermaid.js.
This module includes a lot of TODOs - please could someone take a look at it and add some more content (learning objectives and prerequisites at a minimum).
Also: why is the title "Image Math" and not "Convolution Filters" or similar?alpha releasehttps://git.embl.de/grp-bio-it/image-analysis-training-resources/-/merge_requests/45WIP: convert Morphological Filters module to proper layout2020-04-23T14:33:19ZToby HodgesWIP: convert Morphological Filters module to proper layout@tischer @halavaty @hossain Please could one of you take a look at this and try to fill in some of the TODOs? In particular, this module still needs:
- [ ] more detail in the "Motivation" section
- [ ] platform-specific exercises
- [ ] ...@tischer @halavaty @hossain Please could one of you take a look at this and try to fill in some of the TODOs? In particular, this module still needs:
- [ ] more detail in the "Motivation" section
- [ ] platform-specific exercises
- [ ] links to appropriate "Learn Next" modules
- [ ] a figure/diagram to illustrate the concept?
You can see a built version at https://stamper.embl-community.io/image-analysis-training-resources/filter_morphologicalalpha releasehttps://git.embl.de/grp-bio-it/image-analysis-training-resources/-/merge_requests/50WIP: Converting Difference of Gaussians module2020-04-23T14:32:10ZToby HodgesWIP: Converting Difference of Gaussians module- [x] convert module to new layout
- [x] convert concept map to `Mermaid.js`
- [ ] add learning objectives
- [ ] add prerequisites
- [ ] add motivation
- [ ] add explanatory diagram (optional)
- [ ] add exercises
- [ ] add links to modul...- [x] convert module to new layout
- [x] convert concept map to `Mermaid.js`
- [ ] add learning objectives
- [ ] add prerequisites
- [ ] add motivation
- [ ] add explanatory diagram (optional)
- [ ] add exercises
- [ ] add links to modules to learn nextalpha releasehttps://git.embl.de/grp-bio-it/image-analysis-training-resources/-/merge_requests/48Fix error in Jekyll logic2019-07-26T09:29:19ZToby HodgesFix error in Jekyll logicCloses #61
Closes #60
The Jekyll+JS mix was missing an `{% if ... %}` tag, which was causing weird behaviour when a module had platform-specific activities but no platform-specific exercises.Closes #61
Closes #60
The Jekyll+JS mix was missing an `{% if ... %}` tag, which was causing weird behaviour when a module had platform-specific activities but no platform-specific exercises.Toby HodgesToby Hodgeshttps://git.embl.de/grp-bio-it/image-analysis-training-resources/-/merge_requests/47Resolve "Activities shown without explicitly selecting one"2019-07-26T09:22:41ZToby HodgesResolve "Activities shown without explicitly selecting one"This should fix issue 61 in the main repoThis should fix issue 61 in the main repohttps://git.embl.de/grp-bio-it/image-analysis-training-resources/-/merge_requests/46Add KNIME activities2019-07-25T14:15:02Z Stefan HelfrichAdd KNIME activitiesThis merge request adds KNIME activities for the following modules:
* Binarization
* Connected components
* Neighborhood filters
The workflow images of the activities are currently directly linked to their KNIME Hub page. That is, those...This merge request adds KNIME activities for the following modules:
* Binarization
* Connected components
* Neighborhood filters
The workflow images of the activities are currently directly linked to their KNIME Hub page. That is, those activities will not be available/shown when some is looking to run an offline training.https://git.embl.de/grp-bio-it/image-analysis-training-resources/-/merge_requests/44Style polishing2019-07-24T13:56:34ZToby HodgesStyle polishingCleaning up the style a bit more
Fixes #56
Fixes #48
Fixes #24 Cleaning up the style a bit more
Fixes #56
Fixes #48
Fixes #24 https://git.embl.de/grp-bio-it/image-analysis-training-resources/-/merge_requests/38Carpentries style2019-07-24T10:34:07ZToby HodgesCarpentries styleStill to do before merging:
- [x] remove superfluous Carpentries-related image files
- [x] clean up homepage styling
- [ ] add conditional to module layout to center-align concept map when no example figure is presentStill to do before merging:
- [x] remove superfluous Carpentries-related image files
- [x] clean up homepage styling
- [ ] add conditional to module layout to center-align concept map when no example figure is presentToby HodgesToby Hodgeshttps://git.embl.de/grp-bio-it/image-analysis-training-resources/-/merge_requests/42Pixels2019-07-18T11:50:37ZChristian TischerPixelsAliaksandr HalavatyiAliaksandr Halavatyihttps://git.embl.de/grp-bio-it/image-analysis-training-resources/-/merge_requests/43Improve nbh2019-07-18T09:42:52ZChristian TischerImprove nbhAliaksandr HalavatyiAliaksandr Halavatyihttps://git.embl.de/grp-bio-it/image-analysis-training-resources/-/merge_requests/40Pixel neighbourhood conversion2019-07-18T09:30:08ZAliaksandr HalavatyiPixel neighbourhood conversionRefactoring pixel neighbourhood moduleRefactoring pixel neighbourhood moduleChristian TischerChristian Tischerhttps://git.embl.de/grp-bio-it/image-analysis-training-resources/-/merge_requests/39Connected components2019-07-18T08:59:07ZChristian TischerConnected componentsChanged to new structureChanged to new structureAliaksandr HalavatyiAliaksandr Halavatyihttps://git.embl.de/grp-bio-it/image-analysis-training-resources/-/merge_requests/37Add initial python materials2019-07-18T06:27:05ZConstantin PapeAdd initial python materialsAdds a python activity for binarization, including links to statically hosted jupyter notebook and binder hosted jupyter notebook from [here](https://github.com/embl-bio-it/image-analysis-with-python/blob/carpentry/image-analysis-session...Adds a python activity for binarization, including links to statically hosted jupyter notebook and binder hosted jupyter notebook from [here](https://github.com/embl-bio-it/image-analysis-with-python/blob/carpentry/image-analysis-session/image-binarization.ipynb).https://git.embl.de/grp-bio-it/image-analysis-training-resources/-/merge_requests/36Set a default platform for exercises & activities2019-07-04T10:26:27ZToby HodgesSet a default platform for exercises & activitiesFixes #45Fixes #45https://git.embl.de/grp-bio-it/image-analysis-training-resources/-/merge_requests/34add default option with no displayed div for activities and exercises2019-06-24T15:27:59ZToby Hodgesadd default option with no displayed div for activities and exercisesFixes #31
check out the working test version here: https://stamper.embl-community.io/image-analysis-training-resources/modules/binarization.htmlFixes #31
check out the working test version here: https://stamper.embl-community.io/image-analysis-training-resources/modules/binarization.htmlChristian TischerChristian Tischerhttps://git.embl.de/grp-bio-it/image-analysis-training-resources/-/merge_requests/35add pipeline status badge to README2019-06-24T09:11:15ZToby Hodgesadd pipeline status badge to READMEhttps://git.embl.de/grp-bio-it/image-analysis-training-resources/-/merge_requests/29WIP: Binarization concept2019-06-18T07:33:48ZChristian TischerWIP: Binarization conceptI found that our binarization concept map was actually an "apply threshold" concept map and I tried improving this. Below is my current version.
Suggestions for further improvements are welcome.
E.g., it would be nice if the `Apply inte...I found that our binarization concept map was actually an "apply threshold" concept map and I tried improving this. Below is my current version.
Suggestions for further improvements are welcome.
E.g., it would be nice if the `Apply intensity threshold` was visually on the same height as as `Binarization algorithm`, but I did not know how to achieve this.
```mermaid
graph TD
PV(Intensity pixel values) --> A(Binarization algorithm)
A --> BPV(Binary pixel values)
BPV --> BG("Background (0)")
BPV --> FG("Foreground (1, 255)")
A --- |e.g.|B(Apply intensity threshold)
```
```
graph TD
PV(Intensity pixel values) --> A(Binarization algorithm)
A --> BPV(Binary pixel values)
BPV --> BG("Background (0)")
BPV --> FG("Foreground (1, 255)")
A --- |e.g.|B(Apply intensity threshold)
```Aliaksandr HalavatyiAliaksandr Halavatyihttps://git.embl.de/grp-bio-it/image-analysis-training-resources/-/merge_requests/33Update modules2019-06-18T06:08:34ZChristian TischerUpdate modulesI am adding here all the changes from the markdown branch to the master branch, such that the master branch is now up to date.I am adding here all the changes from the markdown branch to the master branch, such that the master branch is now up to date.Aliaksandr HalavatyiAliaksandr Halavatyi