image-analysis-training-resources issueshttps://git.embl.de/grp-bio-it/image-analysis-training-resources/-/issues2019-07-24T09:51:00Zhttps://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/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/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/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-downhttps://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/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/22add python code examples2019-07-27T07:18:08ZChristian Tischeradd python code examplesalpha releasehttps://git.embl.de/grp-bio-it/image-analysis-training-resources/-/issues/19review object_splitting module2019-07-27T07:18:08ZChristian Tischerreview object_splitting module@hossain, would you like to review the module: object_splitting.md?
Maybe this should be renamed into "watershed"?
Maybe this could be split into several modules?@hossain, would you like to review the module: object_splitting.md?
Maybe this should be renamed into "watershed"?
Maybe this could be split into several modules?alpha releaseM. Julius HossainM. Julius Hossainhttps://git.embl.de/grp-bio-it/image-analysis-training-resources/-/issues/18split up rank filter module2019-07-18T12:49:50ZChristian Tischersplit up rank filter moduleThis module is quite big and could be split up in several smaller modules:
`../modules/filter_rank.md`
@halavaty, is that something you'd be interested to do? And, of course, be invited to improve the module(s) as you like.This module is quite big and could be split up in several smaller modules:
`../modules/filter_rank.md`
@halavaty, is that something you'd be interested to do? And, of course, be invited to improve the module(s) as you like.Aliaksandr HalavatyiAliaksandr Halavatyihttps://git.embl.de/grp-bio-it/image-analysis-training-resources/-/issues/16image calibration2019-05-29T08:54:45ZChristian Tischerimage calibration- Do images also have a calibration in MATLAB?
- Do images also have a calibration in python?- Do images also have a calibration in MATLAB?
- Do images also have a calibration in python?M. Julius HossainM. Julius Hossainhttps://git.embl.de/grp-bio-it/image-analysis-training-resources/-/issues/9Advanced material on object segmentation/splitting2019-04-08T08:03:36ZAliaksandr HalavatyiAdvanced material on object segmentation/splittingI suggest to add links for *active contours*/*level sets* as *Learn more* either in the material about segmentation or in the workshop *object splitting*
Possible links are:
- https://www.intechopen.com/books/medical-and-biological-image...I suggest to add links for *active contours*/*level sets* as *Learn more* either in the material about segmentation or in the workshop *object splitting*
Possible links are:
- https://www.intechopen.com/books/medical-and-biological-image-analysis/active-contour-based-segmentation-techniques-for-medical-image-analysis
- https://en.wikipedia.org/wiki/Level-set_method
- https://imagej.net/Level_Setshttps://git.embl.de/grp-bio-it/image-analysis-training-resources/-/issues/8Formative assesment2019-07-27T07:18:08ZAliaksandr HalavatyiFormative assesmenthttps://git.embl.de/grp-bio-it/image-analysis-training-resources/blob/master/workshops/image-feature-enhancement.md#formative-assessment
Never before met the term *Formative assesment*. Maybe better term can be found?https://git.embl.de/grp-bio-it/image-analysis-training-resources/blob/master/workshops/image-feature-enhancement.md#formative-assessment
Never before met the term *Formative assesment*. Maybe better term can be found?alpha releasehttps://git.embl.de/grp-bio-it/image-analysis-training-resources/-/issues/6image dump2019-04-11T06:02:08ZChristian Tischerimage dump![image](/uploads/284ad5edadf96234037f895a86338a58/image.png)![image](/uploads/284ad5edadf96234037f895a86338a58/image.png)