Image Data Explorer issueshttps://git.embl.de/heriche/image-data-explorer/-/issues2023-07-11T14:30:16Zhttps://git.embl.de/heriche/image-data-explorer/-/issues/37Preparing the data instructions2023-07-11T14:30:16ZChristian TischerPreparing the data instructions@heriche
That does not work out of the box:
` (head -1 fileA.csv && tail -n +2 -q file*.csv) >> ../table.csv`
I guess `fileA.csv` and `file*.csv` should be replaced by something? Maybe just `*.csv`?
----
I am also not sure about th...@heriche
That does not work out of the box:
` (head -1 fileA.csv && tail -n +2 -q file*.csv) >> ../table.csv`
I guess `fileA.csv` and `file*.csv` should be replaced by something? Maybe just `*.csv`?
----
I am also not sure about the `../table.csv` instead of `table.csv`, because if there are relative paths in the tables, moving the table into another directory might invalidate those paths?! Ah OK, if you say that one anyway has to explicitly give the image root dir than this does not matter, but I sometimes assume the paths to be relative to the table location.https://git.embl.de/heriche/image-data-explorer/-/issues/35Read (ROI of) OME-Zarr2023-05-24T08:34:30ZChristian TischerRead (ROI of) OME-Zarr@heriche is there a way to read data from (OME-)Zarr in R?@heriche is there a way to read data from (OME-)Zarr in R?https://git.embl.de/heriche/image-data-explorer/-/issues/33Server does not work2022-02-04T08:40:47ZChristian TischerServer does not work> The app is then accessible from a web browser at http://127.0.0.1:5476
Gives me an "unable to connect"> The app is then accessible from a web browser at http://127.0.0.1:5476
Gives me an "unable to connect"Jean-Karim HericheJean-Karim Herichehttps://git.embl.de/heriche/image-data-explorer/-/issues/31Container can't read images2021-02-24T19:49:33ZJean-Karim HericheContainer can't read imagesContainers for v0.8 and v0.9 are unable to read/display images producing instead some java errors such as
- Error in .jcall: java.lang.StackOverflowError
- Java Exception <no description because toString() failed>.jfindClass(cl)new("job...Containers for v0.8 and v0.9 are unable to read/display images producing instead some java errors such as
- Error in .jcall: java.lang.StackOverflowError
- Java Exception <no description because toString() failed>.jfindClass(cl)new("jobjRef", jobj = <pointer: 0x55c991b1b3f0>, jclass = "java/lang/Throwable")
- Error in .jcall("java/lang/Class", "Ljava/lang/Class;", "forName, cl, : RcallMethod: cannot determine object class
Error in .jfindClass: Java Exception <no description because toString() failed> jfindClass(cl)new("jobjRef", jobj = <pointer: 0x55c99cdba3e8>, jclass = "java/lang/Throwable")https://git.embl.de/heriche/image-data-explorer/-/issues/30Find discriminative features based on annotation2020-11-18T20:44:36ZChristian TischerFind discriminative features based on annotation@heriche
There is something that I need for almost every project: Given some class annotations I would like to know which of the measured features are most useful to distinguish the different classes. Could we add something for this to...@heriche
There is something that I need for almost every project: Given some class annotations I would like to know which of the measured features are most useful to distinguish the different classes. Could we add something for this to the IDE?
For example, maybe a visualisation (could be pure text if there is nothing graphical) of the best decision tree? This would have the additional benefit that one could also see at which threshold values the features should be used to distinguish the classes.
CellProfiler Analyst does something very similar:
https://www.ncbi.nlm.nih.gov/books/NBK126174/figure/hcsimage.F8/
![image](/uploads/20856a59e09773f3d5fd9824e52972f2/image.png)https://git.embl.de/heriche/image-data-explorer/-/issues/29Complete documentation regarding annotation process2021-06-02T07:11:24ZJean-Karim HericheComplete documentation regarding annotation processhttps://git.embl.de/heriche/image-data-explorer/-/issues/28Annotation2020-10-27T16:47:05ZChristian TischerAnnotationMaybe I am doing something wrong but maybe the annotator could be improved a bit.
Suggestions/Questions:
1. Is it possible to select multiple cells in the image at once and batch annotate them?
2. Would it be possible to have a dedicate...Maybe I am doing something wrong but maybe the annotator could be improved a bit.
Suggestions/Questions:
1. Is it possible to select multiple cells in the image at once and batch annotate them?
2. Would it be possible to have a dedicated annotation tab where small crops containing one cell at a time are presented one by one and then the user could annotate (e.g. via keyboard shortcut) and then the next one would be shown automatically?https://git.embl.de/heriche/image-data-explorer/-/issues/27Image viewer navigation2021-06-02T07:09:51ZChristian TischerImage viewer navigation@heriche
How do I drag the image in the image viewer when I am zoomed in?
Maybe we should have a little section for how to use the viewer?@heriche
How do I drag the image in the image viewer when I am zoomed in?
Maybe we should have a little section for how to use the viewer?https://git.embl.de/heriche/image-data-explorer/-/issues/26Image root dir2020-10-23T08:16:09ZChristian TischerImage root dirWhat about auto-filling this field with the folder in which the table is?What about auto-filling this field with the folder in which the table is?https://git.embl.de/heriche/image-data-explorer/-/issues/25Error during startup2020-10-22T16:15:08ZChristian TischerError during startup```
> shiny::runApp("image_data_explorer.R", host = "0.0.0.0", port = 5476)
Loading required package: shiny
Installing devtools
Installing BiocManager
Installing shinyFiles
Installing shinycssloaders
Installing shinydashboard
Installing ...```
> shiny::runApp("image_data_explorer.R", host = "0.0.0.0", port = 5476)
Loading required package: shiny
Installing devtools
Installing BiocManager
Installing shinyFiles
Installing shinycssloaders
Installing shinydashboard
Installing shinyWidgets
Installing shinybusy
Installing RANN
Installing uwot
Error in contrib.url(repos, "source") :
trying to use CRAN without setting a mirror
Calls: <Anonymous> ... ..stacktraceon.. -> install.packages -> contrib.url
Execution halted
```
@heriche any ideas?https://git.embl.de/heriche/image-data-explorer/-/issues/24Multi-channel image support2021-06-02T11:00:12ZChristian TischerMulti-channel image support@heriche
From the documentation: `Each image file must contain an image of at most 3 dimensions with the third dimension representing either depth (z coordinate) or time.`
What happens if the 3rd dimension is channels?@heriche
From the documentation: `Each image file must contain an image of at most 3 dimensions with the third dimension representing either depth (z coordinate) or time.`
What happens if the 3rd dimension is channels?https://git.embl.de/heriche/image-data-explorer/-/issues/23Open images in ImageJ2022-10-07T07:18:46ZChristian TischerOpen images in ImageJ@heriche
cc @halavaty @ext.hmbotelho
Could that maybe work for us?
- https://github.com/imjoy-team/imagej.js#sharing-images-macro-or-plugins-with-url-parameters
See also this thread:
- https://forum.image.sc/t/open-an-image-in-imagej...@heriche
cc @halavaty @ext.hmbotelho
Could that maybe work for us?
- https://github.com/imjoy-team/imagej.js#sharing-images-macro-or-plugins-with-url-parameters
See also this thread:
- https://forum.image.sc/t/open-an-image-in-imagej-js-via-http-api/44274https://git.embl.de/heriche/image-data-explorer/-/issues/22Support multi table input2021-06-02T07:14:09ZChristian TischerSupport multi table input@heriche @ext.hmbotelho @halavaty
What do you think about supporting as an input multiple tables, e.g., all table files in one folder?
I am asking because I think this will be very prevalent. Essentially all image batch analysis (espe...@heriche @ext.hmbotelho @halavaty
What do you think about supporting as an input multiple tables, e.g., all table files in one folder?
I am asking because I think this will be very prevalent. Essentially all image batch analysis (especially computer cluster based) will naturally have one table per image as an output. It would be nice if the table merging step would not have to happen outside the IDE.https://git.embl.de/heriche/image-data-explorer/-/issues/21Crashes when clicking on image if no ROI is defined2020-09-21T08:35:07ZJean-Karim HericheCrashes when clicking on image if no ROI is definedHappens with the screen_example test dataHappens with the screen_example test datahttps://git.embl.de/heriche/image-data-explorer/-/issues/20Dealing with large number of data points2021-06-02T07:23:44ZJean-Karim HericheDealing with large number of data pointsData tables with a large number of rows pose three problems:
1. They can exceed upload file size limits. There is a limit in the app but there may also be one in the web browser used and on the server hosting the app.
2. The app performa...Data tables with a large number of rows pose three problems:
1. They can exceed upload file size limits. There is a limit in the app but there may also be one in the web browser used and on the server hosting the app.
2. The app performance gets degraded. Although this is partly dependent on the set up (i.e. hardware, network), it's acceptable with 15000 rows and still usable but noticeably slower with 100000.
3. Points pile up on top of each other in the plot. This obscures use of different colours and makes selecting a particular point impossible. Zooming in only partially alleviates the issue because it only works when there aren't too many points in the zoomed in area.https://git.embl.de/heriche/image-data-explorer/-/issues/19License2020-09-21T12:52:41ZJean-Karim HericheLicenseThe project needs a license otherwise it can't legally be re-used. R and Shiny and other packages the project uses are released under the GPL-3 license but I think we can use others. Anyone has an opinion or preference about which licens...The project needs a license otherwise it can't legally be re-used. R and Shiny and other packages the project uses are released under the GPL-3 license but I think we can use others. Anyone has an opinion or preference about which license to use?https://git.embl.de/heriche/image-data-explorer/-/issues/18Dimensionality reduction: duplicate columns2020-07-08T08:25:55ZJean-Karim HericheDimensionality reduction: duplicate columnsWhen running the same algorithm multiple times (usually to try different parameters), either new columns should be created with unique names or the columns created the first time should be re-used. To prevent the table from growing too m...When running the same algorithm multiple times (usually to try different parameters), either new columns should be created with unique names or the columns created the first time should be re-used. To prevent the table from growing too much, I prefer re-using columns. For this, column names need to be standardized. For PCA, I propose to use PCA.PC1 and PCA.PC2 and for UMAP, UMAP.X1 and UMAP.X2. Upon a click on the "Apply" button, the app should check if they already exist, if not, create them, else populate them with the result of the computation.https://git.embl.de/heriche/image-data-explorer/-/issues/17Dimensionality reduction: text2020-07-08T09:29:56ZJean-Karim HericheDimensionality reduction: textTo avoid confusion, the boxes should have unambiguous and clear titles and text:
* The first box should be named either columns or features or variables but not a combination of these terms, the text should make clear that the algorithm ...To avoid confusion, the boxes should have unambiguous and clear titles and text:
* The first box should be named either columns or features or variables but not a combination of these terms, the text should make clear that the algorithm will be applied to the variables represented by these columns.
* Don't use abbreviations in the text (e.g. algo) unless they are in common use (e.g. PCA) also because this makes it look less professional :)
* The box to input parameters for the dimensionality reduction algorithm should be named "parameters".
In general names should be used consistently and new terms should not be introduced unnecessarily. For example, the content of a column is referred to as a variable in the input data section but the term feature has not been used so far.https://git.embl.de/heriche/image-data-explorer/-/issues/16Crashes when changing data set2020-10-27T16:50:03ZJean-Karim HericheCrashes when changing data setThere may be several causes but a possible fix could be to reinitialize all reactive values upon loading a new data table.There may be several causes but a possible fix could be to reinitialize all reactive values upon loading a new data table.https://git.embl.de/heriche/image-data-explorer/-/issues/15Standardising column names2020-09-11T09:58:06ZJean-Karim HericheStandardising column namesWhat are the columns we need and can we define a standard name for them?What are the columns we need and can we define a standard name for them?