image-analysis-training-resources issueshttps://git.embl.de/grp-bio-it/image-analysis-training-resources/-/issues2020-04-23T14:12:07Zhttps://git.embl.de/grp-bio-it/image-analysis-training-resources/-/issues/42next hackathon2020-04-23T14:12:07ZChristian Tischernext hackathon@hossain
@halavaty
Could we make an appointment for another day where we work on it?
At some point in July or August?@hossain
@halavaty
Could we make an appointment for another day where we work on it?
At some point in July or August?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/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/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/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/37Binarization MATLAB2020-04-23T14:16:20ZChristian TischerBinarization MATLABThe MATLAB code for image binarization contains a `function`.
Is that necessary? Since MATLAB is a scripting language I think the code should also run without a function, or? If so, I would remove the function, because it makes it more c...The MATLAB code for image binarization contains a `function`.
Is that necessary? Since MATLAB is a scripting language I think the code should also run without a function, or? If so, I would remove the function, because it makes it more complicated than necessary.M. Julius HossainM. Julius Hossainhttps://git.embl.de/grp-bio-it/image-analysis-training-resources/-/issues/36Further material2019-06-12T10:42:11ZChristian TischerFurther material- Tischi's iBiology Talk
- MOOPS- Tischi's iBiology Talk
- MOOPSChristian 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/34Literature2019-06-11T19:03:12ZChristian TischerLiterature- https://cecas.clemson.edu/~stb/ece847/internal/cvbook/ch02_pixproc.pdf- https://cecas.clemson.edu/~stb/ece847/internal/cvbook/ch02_pixproc.pdfChristian TischerChristian Tischerhttps://git.embl.de/grp-bio-it/image-analysis-training-resources/-/issues/33rank filter activities2019-06-12T06:16:58ZChristian Tischerrank filter activities@halavaty
I do not remember exactly what we discussed to have as activities for this module:
https://git.embl.de/grp-bio-it/image-analysis-training-resources/blob/markdown/modules/filter_rank.md
Having the median filter as an example ...@halavaty
I do not remember exactly what we discussed to have as activities for this module:
https://git.embl.de/grp-bio-it/image-analysis-training-resources/blob/markdown/modules/filter_rank.md
Having the median filter as an example on a grayscale image makes a lot of sense because one can then use this to then introduce median based local bg subtraction, e.g. in the next module.
But did we have other meaningful ideas?https://git.embl.de/grp-bio-it/image-analysis-training-resources/-/issues/32Binarization exercise2019-06-10T21:04:35ZChristian TischerBinarization exercise@halavaty @hossain
I am struggling to find a binarization exercise that has the right level.
Either I feel they are too easy or I feel they sneakily require new concepts.
This is my current attempt (https://git.embl.de/grp-bio-it/ima...@halavaty @hossain
I am struggling to find a binarization exercise that has the right level.
Either I feel they are too easy or I feel they sneakily require new concepts.
This is my current attempt (https://git.embl.de/grp-bio-it/image-analysis-training/resources/blob/binarizationExercise/modules/binarization.md):
- Open image: "xy_8bit__binarization_exercise.tif".
- How many 'signficiantly different' (by more than 10 gray values) threshold values can you find such that there is exactly one connected foreground region?
<details>
<summary>Solution</summary>
There are four such threshold values, e.g. 8, 46, 94, and 111. There are more, but they are within 10 gray values of those four and thus, according to the rules of this exercise, do not count as significantly different.
</details>
<br>
<br>
The issue could be that one kind of needs the concept of a "connected" region (possibly raising the 4- vs 8-connected issue) and it also somewhat introduces a "noise" concept. But maybe that's fine, or even good because it would motivate the "Learn next" modules? I am not sure. Maybe it is not appropriate and one should find something easier...?!https://git.embl.de/grp-bio-it/image-analysis-training-resources/-/issues/31Additional, platform specific exercises2019-06-24T15:27:59ZChristian TischerAdditional, platform specific exercises@stamper @halavaty
I find this visually a bit distracting, i.e. too much information.
Could we somehow change this such that one only sees those additional exercises on demand.
Maybe we could have one drop-down value "None selected" a...@stamper @halavaty
I find this visually a bit distracting, i.e. too much information.
Could we somehow change this such that one only sees those additional exercises on demand.
Maybe we could have one drop-down value "None selected" as a default, where there is nothing shown?
As an example, see below screenshot. I think it would be nice if the part below "Perform additional ..." would **not** be visible by default:
![image](/uploads/7f5224cfce399198e940a38c1dcf91b3/image.png)https://git.embl.de/grp-bio-it/image-analysis-training-resources/-/issues/30Binarization module needs updating2019-06-07T11:45:45ZToby HodgesBinarization module needs updatingNow that I'm done abusing it for my experiments with Jekyll, the module on image binarization needs to be updated to be more appropriate. Can someone who knows more about this stuff than I do @tischer @halavaty @hossain help out here, pl...Now that I'm done abusing it for my experiments with Jekyll, the module on image binarization needs to be updated to be more appropriate. Can someone who knows more about this stuff than I do @tischer @halavaty @hossain help out here, please?https://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/28Module rendering: Space between selection and content2019-06-07T17:42:51ZChristian TischerModule rendering: Space between selection and content@stamper
1. Would it be possible to add one line (space) between the drop-down and the content?
![image](/uploads/1c905b9cfc6c7f3899abdd395f4a35e5/image.png)
1. Same for the formative assessment
1. If you point me to the file where suc...@stamper
1. Would it be possible to add one line (space) between the drop-down and the content?
![image](/uploads/1c905b9cfc6c7f3899abdd395f4a35e5/image.png)
1. Same for the formative assessment
1. If you point me to the file where such a space could be added I'd love to do it myself in order to get a bit into the Jekyll stuff!Christian TischerChristian Tischerhttps://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/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/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/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/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`...