Image Data Explorer issueshttps://git.embl.de/heriche/image-data-explorer/-/issues2020-09-11T09:58:06Zhttps://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?https://git.embl.de/heriche/image-data-explorer/-/issues/6Plotly (too) slow2020-06-22T10:29:41ZJean-Karim HerichePlotly (too) slowI've done a quick test and plotly is definitely slow. This becomes already noticeable with a "small" data set of 2500 2d points. Digging into it a bit, it seems this may be because plotly serializes the data to json before plotting.
Do w...I've done a quick test and plotly is definitely slow. This becomes already noticeable with a "small" data set of 2500 2d points. Digging into it a bit, it seems this may be because plotly serializes the data to json before plotting.
Do we expect to have to deal with larger data sets in the future ?https://git.embl.de/heriche/image-data-explorer/-/issues/41Enable annotations in multiple columns2023-09-12T06:20:40ZJean-Karim HericheEnable annotations in multiple columnsFrom Nathan Stutzman (nbstutzman@ucsd.edu) by email:
> **Multiple Annotations**: There are several aspects I would like to annotate about my data. Right now it only allows me to annotate one column at a time; to annotate a different colu...From Nathan Stutzman (nbstutzman@ucsd.edu) by email:
> **Multiple Annotations**: There are several aspects I would like to annotate about my data. Right now it only allows me to annotate one column at a time; to annotate a different column I have to go back to the Annotation page. It would be nice to be able to annotate multiple columns while I'm looking at the same image.https://git.embl.de/heriche/image-data-explorer/-/issues/40Visualize secondary grouping2023-09-12T06:09:31ZJean-Karim HericheVisualize secondary groupingFrom Nathan Stutzman (nbstutzman@ucsd.edu) by email:
> **Secondary Grouping**: For a lot of my data, I have two dimensions in my grouping scheme and it would be nice to visualize both at the same time. For example, my primary grouping ma...From Nathan Stutzman (nbstutzman@ucsd.edu) by email:
> **Secondary Grouping**: For a lot of my data, I have two dimensions in my grouping scheme and it would be nice to visualize both at the same time. For example, my primary grouping may be by treatment, but I may also be comparing those treatments across timepoints. Right now the best way I can visualize both at once is to group by one and then filter/select by the other grouping, but this isn't the best since I can only show one selection at a time and the selected points black out the other grouping.https://git.embl.de/heriche/image-data-explorer/-/issues/39Document launch_IDE.R2023-07-11T14:36:53ZJean-Karim HericheDocument launch_IDE.RDocument use of script [launch_IDE.R](https://git.embl.de/heriche/image-data-explorer/-/blob/master/launch_IDE.R)Document use of script [launch_IDE.R](https://git.embl.de/heriche/image-data-explorer/-/blob/master/launch_IDE.R)https://git.embl.de/heriche/image-data-explorer/-/issues/38Document toml config file2023-07-11T14:35:00ZJean-Karim HericheDocument toml config fileDocument the configuration parameters available in template [settings_template.toml](https://git.embl.de/heriche/image-data-explorer/-/blob/master/settings_template.toml)Document the configuration parameters available in template [settings_template.toml](https://git.embl.de/heriche/image-data-explorer/-/blob/master/settings_template.toml)https://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/36Show object from bounding box2023-05-24T08:34:30ZJean-Karim HericheShow object from bounding boxIf the user selects data table columns defining a bounding box, the IDE should extract the corresponding region and display it.
Considerations:
- This requires a bounding box/ROI standard definition. The simplest would be one column ...If the user selects data table columns defining a bounding box, the IDE should extract the corresponding region and display it.
Considerations:
- This requires a bounding box/ROI standard definition. The simplest would be one column for each of min(x), max(x), min(y), max(y), min(z or t) and max(z or t).
- This may have to be limited to some image formats (e.g. ome-zarr) for performance reasons.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/34Handling of large images2022-06-24T07:36:18ZJean-Karim HericheHandling of large imagesLarge images (e.g. EM images) take too long to display.Large images (e.g. EM images) take too long to display.Jean-Karim HericheJean-Karim Herichehttps://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/32Get images from OMERO2021-06-02T10:07:59ZJean-Karim HericheGet images from OMEROIt should be possible to get images from an OMERO database via the [rOMERO.gateway package](https://github.com/ome/rOMERO-gateway).It should be possible to get images from an OMERO database via the [rOMERO.gateway package](https://github.com/ome/rOMERO-gateway).https://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?