Bio-IT issueshttps://git.embl.de/groups/grp-bio-it/-/issues2021-10-19T15:23:03Zhttps://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 5https://git.embl.de/grp-bio-it/docs/-/issues/9Add page TOC2020-07-15T14:49:52ZToby HodgesAdd page TOCTo make navigation within pages easier, add a TOC to the beginning of every page that links to every second-level heading in the page contentTo make navigation within pages easier, add a TOC to the beginning of every page that links to every second-level heading in the page contentToby HodgesToby Hodgeshttps://git.embl.de/grp-bio-it/docs/-/issues/11fix checklist formatting2020-07-14T14:42:06ZToby Hodgesfix checklist formattingformatting on checklists - in particular those with nested list items - is really bad. See e.g. https://grp-bio-it.embl-community.io/docs/checklists/bioit_lunch/ and https://grp-bio-it.embl-community.io/docs/checklists/cofest/formatting on checklists - in particular those with nested list items - is really bad. See e.g. https://grp-bio-it.embl-community.io/docs/checklists/bioit_lunch/ and https://grp-bio-it.embl-community.io/docs/checklists/cofest/Toby HodgesToby Hodgeshttps://git.embl.de/grp-bio-it/docs/-/issues/13add cuckoo.team to useful links list2020-07-13T13:35:48ZToby Hodgesadd cuckoo.team to useful links listhttps://git.embl.de/grp-bio-it/image-analysis-training-resources/-/issues/4We need a project image2020-04-23T14:30:00ZToby HodgesWe need a project imageLow priority, but the project repository needs an image (a "project avatar").Low priority, but the project repository needs an image (a "project avatar").alpha releasehttps://git.embl.de/grp-bio-it/image-analysis-training-resources/-/issues/1Consider adding guidance/requirements for inclusion of example images2020-04-23T14:29:39ZToby HodgesConsider adding guidance/requirements for inclusion of example images> All of these images are freely available and chosen according to availability of good quality metadata associated with the image.> All of these images are freely available and chosen according to availability of good quality metadata associated with the image.https://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/38Image Display Exercise2020-04-23T14:28:56ZChristian TischerImage Display ExerciseAdd exercise to open two images and show them next to each other with the same LUT settings.
(Save those images with ImageJ such that they do initially don't have the same LUT settings).Add exercise to open two images and show them next to each other with the same LUT settings.
(Save those images with ImageJ such that they do initially don't have the same LUT settings).Christian TischerChristian Tischerhttps://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/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/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/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/27introducing image calibration2020-04-23T14:24:57ZChristian Tischerintroducing image calibration@halavaty
We could merge those two modules into one?
https://git.embl.de/grp-bio-it/image-analysis-training-resources/blob/markdown/modules/image_pixel_content.md
https://git.embl.de/grp-bio-it/image-analysis-training-resources/blob/m...@halavaty
We could merge those two modules into one?
https://git.embl.de/grp-bio-it/image-analysis-training-resources/blob/markdown/modules/image_pixel_content.md
https://git.embl.de/grp-bio-it/image-analysis-training-resources/blob/markdown/modules/calibration.md
Not sure it would be too much information?
I would not like to remove the 3D aspect, because also all the downstream modules work on both 2D and 3D data.
That is, I do not distinguish much between 2D and 3D images, because I think all the concepts work for 2D and 3D, thus there is no need to repeat everything later for 3D (rather always immediately also do in 3D seems better to me).https://git.embl.de/grp-bio-it/image-analysis-training-resources/-/issues/44Modules about Hessians2020-04-23T14:24:19ZChristian TischerModules about HessiansMake modules about using Hessian's for image analysis.
## Literature
- [Frangi](https://dspace.library.uu.nl/bitstream/handle/1874/377/c2.pdf;jsessionid=89DED7829B8D72D450076EC58459EA77?sequence=18)
- [Jerman](https://www.researchgate....Make modules about using Hessian's for image analysis.
## Literature
- [Frangi](https://dspace.library.uu.nl/bitstream/handle/1874/377/c2.pdf;jsessionid=89DED7829B8D72D450076EC58459EA77?sequence=18)
- [Jerman](https://www.researchgate.net/publication/283558933_Beyond_Frangi_An_improved_multiscale_vesselness_filter)Christian TischerChristian Tischerhttps://git.embl.de/grp-bio-it/image-analysis-training-resources/-/issues/35Add general motivation module2020-04-23T14:23:57ZChristian TischerAdd general motivation moduleGet arguments from Pasi's introduction slide.Get arguments from Pasi's introduction slide.alpha releaseChristian TischerChristian Tischerhttps://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/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 release