can you use np.int32 as in the master version here
This is the error you reported previously. Did you try changing all memoryviews (int[:, :] im_fgnd_mask) to explicit declarations like "np.ndarray[np.int32_t, ndim=2] im_fgnd_mask" in https://github.com/DigitalSlideArchive/HistomicsTK/blob/master/histomicstk/segmentation/nuclear/_max_clustering_cython.pyx#L8
For some reason, memoryviews don't seem to work in your environment
Here is a brief tutorial on Cython memory views for some background -- https://cython.readthedocs.io/en/latest/src/userguide/memoryviews.html
But still showing some error:
i wants to generate button in openseadragon viewer for actual zoom level , 5x,10x 15x 20x
is there any opensource code i can find
darkmich, generally, custom metadata searches work best if you write an endpoint that does what you want. That way, if your data would benefit from an index you can ensure the index exists, and you can scope the search to whatever you need. There are plugins that add some search -- for instance there is two branches on the digital_slide_archive that do different metadata searches in different ways ...
When you say you'd like to have a collection require particular metadata, how would you like that enforced? For instance, would you want it to reject adding items if they don't have the correct metadata? Or just not search such items?
You can always use a web browser offline to view annotations. Fundamentally, we wanted to be able have multiple users collaborate on creating annotations and viewing images, so the UI has used javascript and html. The restful python library can be used without the UI (via direct python or via REST calls), but since we can use the existing UI online or offline, we haven't had any need to make it another way.
@manthey I see you’ve some commits to large_image as well. Do you have a suggestion for a branch or tag I should use to get large_image running with histomicsTK in girder2.5 ?
large_image master is still the Girder 2.x branch (and works with HistomicsTK). There is a large_image girder-3 branch. I expect that in the near future (a week or two), that the girder-3 branch will become the new master and there will be a long-standing grider 2.x branch for maintenance.
do you have any idea what the versions/branches/tags of things should be (girder/large_image/histomicsTK) ?
girder-large-image-1.0.0-dev52 from pypi requires girder3,
Large_image master on git is 0.3.0, but doesn’t seem to satisfy HistomicsTK which requires things like 'large-image-source-openslide’, which aren’t the way 0.3.0 are organized.
girder-large-image-1.0.0-dev52 from pypi requires girder3,
Large_image master on git is 0.3.0, but doesn’t seem to satisfy HistomicsTK which requires things like 'large-image-source-openslide’, which aren’t the way 0.3.0 are organized.
HistomicsTK has instructions on installation: https://digitalslidearchive.github.io/HistomicsTK/installation.html . The toolkit is pip installable. The Girder 2.x plugin is not. The easiest way to install it would be via Docker or Vagrant.
Hey, I had a web-viewer based on OpenSeadragon, and I would like to combine the viewer with HistomicsTK and girder to better analysis and manage the whole slide images. I am wondering where I can find the lower level code that called the OpenSeadragon as a function that I can modify, or where I can put that as a plugin, in that case, I can start from there to combine our viewer with Girder. Please see the demo as https://zzzghm.github.io Thank you!
I am attempting to upload an Aperio Imagescope annotation .xml file, associate it with a large_image file, and display the image, with imported annotation, in the HistomicsTK viewer. Is this possible? I know there is a POST /item/{id}/aperio API command to import an item (.xml) as an Aperio annotation and associate it with an image_id but when I go to view the annotations on HistomicsTK after doing so, nothing is present.
This is searchable on specific items via the GET /item/{id}/aperio endpoint, or across items via mongo queries. It isn't exposed on the HistomicsTK interface.
Is there a good tutorial for extending the functionality of the HistomicsTK web-viewer? I understand we need to use the
slicer-cli-web plugin as a template for building in CLI analysis functionality to Girder and linking that to the web interface, but I don't really understand where we are dropping in our custom Python code, and how we build the modified slicer-cli-web plugin into a Docker image, nor how we are supposed to load new plugins. An end-to-end tutorial would be very helpful to more naive users (such as myself) that would like to extend the functionality of the HistomicsTK web interface for their research.
There is a sample on making a CLI analysis plugin here: https://github.com/cdeepakroy/slicer_cli_web_plugin .
@cooperlab Didn't we also have another document explaining how to do this?
There is an example to create a new docker analysis plugin here: https://github.com/cdeepakroy/slicer_cli_web_plugin . There is some information about installing them here: https://digitalslidearchive.github.io/HistomicsTK/installation.html
The test data is downloaded when you run the cmake tests. If you are using the deploy scripts, this should happen via the deploy/test.sh script.
@manthey Following up to your response above, what is the appropriate way to deploy a new Docker image once it has been created, and refresh HistomicsTK/Girder so that it may be used? Particularly with the Docker based HistomicsTK deployment. It seems that existing Docker containers are pulled from Dockerhub, but what about ones we build locally? I see that their is an API endpoint for loading a custom Docker image, but where should that Docker image be built and live? In the case of the Docker deployed HistomicsTK is that within the Docker container that contains the running instance of HistomicsTK?