pickcells-essentials issueshttps://framagit.org/pickcellslab/pickcells-essentials/-/issues2018-11-19T17:49:44Zhttps://framagit.org/pickcellslab/pickcells-essentials/-/issues/37Consider Gabriel Graph for neighbourhoods2018-11-19T17:49:44ZGuillaume BlinConsider Gabriel Graph for neighbourhoodshttps://framagit.org/pickcellslab/pickcells-essentials/-/issues/32Remove LogViewer and replace with Loggers created at runtime for active tasks2022-06-03T11:16:14ZGuillaume BlinRemove LogViewer and replace with Loggers created at runtime for active tasksThe LogViewer currently in coremodules is provided as DefaultDocument and is logging all events irrespective of where they come from. This can make it difficult to understand where log events come from. There are 2 major improvements tha...The LogViewer currently in coremodules is provided as DefaultDocument and is logging all events irrespective of where they come from. This can make it difficult to understand where log events come from. There are 2 major improvements that can be made:
1. LogViewer should not be a DefaultDocument but instead could be available upon user request when clicking a button in a toolbar (maybe bottom toolbar). This means placing Logger views in the container project.
2. Separate logger views could be created at runtime for active tasks (make the button appear in the toolbar when a task is launched). Tasks that have been completed can then be dismissed upon user request. In any case the logs file (in the logs folder of the application) is kept to keep a record of logging eventsUsabilityhttps://framagit.org/pickcellslab/pickcells-essentials/-/issues/29Manual Classification2022-06-03T11:25:39ZGuillaume BlinManual ClassificationA recurrent task when analysing images of embryos is to label several 3D regions so that object features can be extracted for each domain and compared to one another.
Currently the way to go about it is to create a new SegmentationResul...A recurrent task when analysing images of embryos is to label several 3D regions so that object features can be extracted for each domain and compared to one another.
Currently the way to go about it is to create a new SegmentationResult, manually paint the regions using the segmentation editor, compute features, create filters for each unique region and then propagate this classification to other objects using the 'Membership Finder' module and then create new filters again on the target object.
Needless to say that this procedure is **very tedious**.
So here is a feature which would greatly facilitate our lives:
Instead of creating new objects, we could use a modified version of the segmentation editor in order to create a new property in the desired object type:
![image](/uploads/c811ca637ddcdb2e86a8a5e0e0af6879/image.png)
NB: The interface to start looking at in order to implement this is [AnnotationManager](https://framagit.org/pickcellslab/pickcells-api/blob/78686b8f5b62d00aff1a255fd00f6207af054ece/pickcells-img/src/main/java/org/pickcellslab/pickcells/api/img/view/AnnotationManager.java#L46)Usabilityhttps://framagit.org/pickcellslab/pickcells-essentials/-/issues/25Interactive image gallery2022-06-03T12:53:59ZGuillaume BlinInteractive image galleryPickCells allows users to analyse large sets of biological images. The usability evaluation revealed users were often frustrated not to see an overview of their images once imported into PickCells. To solve this, we should add an interac...PickCells allows users to analyse large sets of biological images. The usability evaluation revealed users were often frustrated not to see an overview of their images once imported into PickCells. To solve this, we should add an interactive image gallery.
The user will be able to apply filters and group images based on user-defined categories. We should make sure that this new feature comes with the added benefit of an enriched API allowing plugin developers to easily create and handle image thumbnails (entire images or specific objects detected in images), thus facilitating the development of interactive plugins in the future.
See also pickcellslab/pickcells-api#9UsabilityGuillaume BlinGuillaume Blinhttps://framagit.org/pickcellslab/pickcells-essentials/-/issues/12Association Editor2022-06-03T17:19:17ZGuillaume BlinAssociation EditorThis is a proposal for a new feature which would allow the user to **interactively edit relationships between ImageLocated objects**.
The [TrackEditor](https://framagit.org/pickcellslab/pickcells-essentials/blob/master/pickcells-coremodu...This is a proposal for a new feature which would allow the user to **interactively edit relationships between ImageLocated objects**.
The [TrackEditor](https://framagit.org/pickcellslab/pickcells-essentials/blob/master/pickcells-coremodules/src/main/java/org/pickcellslab/pickcells/tracking/TrackEditor.java) already implements this functionality for TRACK links only. It would be really useful to create a generic version of this.
The initialisation and genericity of this functionality could be implemented by enabling the user to choose 2 options:
1. Choose the type of Links to be edited (with a Predicate on Links to make sure that it connects ImageLocated)
2. Choose an **Association Rule**.
This **'Association Rule'** can be an interface with a linkEdited() method which would trigger rearrangements of other relationships if necessary. For example nuclei to centrosomes associations could be edited this way since associations mistakes may propagate to neighbouring nuclei, corrections would do the same.