NHPatterson
commented
2 years ago Hi Michael,
I'm not sure I have exactly understood your question, but see if this helps...
Shapes are considered 'attachments'. This means they are associated with a particular modality, i.e., you have some annotations made on modality 1 and you want them projected to modality 2 through wsireg's registration.
I have modified the demo code from the github splash readme to add an attachment shape, and then transform it at the end of the run. This will produce a new geojson at the end of the registration. I've broken up the code sections a bit for visibility.
from wsireg.wsireg2d import WsiReg2D
# initialize registration graph
reg_graph = WsiReg2D("my_reg_project", "./project_folder")
# add registration images (modalities)
reg_graph.add_modality(
"modality_fluo",
"./data/im1.tiff",
image_res=0.65,
channel_names=["DAPI", "eGFP", "DsRed"],
channel_colors=["blue", "green", "red"],
prepro_dict={
"image_type": "FL",
"ch_indices": [1],
"as_uint8": True,
"contrast_enhance": True,
},
)
reg_graph.add_modality(
"modality_brightfield",
"./data/im2.tiff",
image_res=1,
prepro_dict={"image_type": "BF", "as_uint8": True, "inv_int_opt": True},
)# new line to add "attachment" shapes to data
reg_graph.add_attachment_shapes("modality_fluo", "fluo_annotations", "./data/fluo_anno.geojson")reg_graph.add_reg_path(
"modality_fluo",
"modality_brightfield",
thru_modality=None,
reg_params=["rigid", "affine"],
)
reg_graph.register_images()
reg_graph.save_transformations()# new line to transform shapes to a new geojson
reg_graph.transform_shapes()reg_graph.transform_images(file_writer="ome.tiff")If you exported the geojson that was transformed from QuPath v0.3.0 or higher (you can do this by going to File -> Object data... -> Export as geojson), you will need to change the file extension from ".json" to ".geojson" (This is a thing that predates QP v0.3.0, I will fix in current wsireg now that you brought to my attention just now, thanks!) and then you can drag and drop it onto the QP canvas and it should load up. All the metadata is maintained: detections should be loaded as detections, annotations as annotations and any measurements should be there, but bear in mind that these are measurements from the previous modality... wsireg simply replaces the coordinate data.
If you are still having issues with drag and drop, this groovy script will prompt you for a file path and then read in the selected geojson. You can run it in the QuPath script editor.
// Import GeoJson into QuPath
// Author : Nathan Heath Patterson, heath.patterson@vanderbilt.edu
// import libraries
import qupath.lib.io.GsonTools
// instantiate tools
def gson=GsonTools.getInstance(true);
// prepare template
def type = new com.google.gson.reflect.TypeToken<List<qupath.lib.objects.PathObject>>() {}.getType();
def json_fp = promptForFile(null)
// read annotations
bufferedReader = new BufferedReader(new FileReader(json_fp));
deserializedAnnotations = gson.fromJson(bufferedReader.text, type);
// add to dataset
addObjects(deserializedAnnotations);
Michael-L-Miller
Awesome project. I'm a novice so was wondering if you could show me how to transform/register the QuPath shapes (Geojson) from one modality to the other. Also, I am having trouble importing these changes into QuPath. Is there a way to apply the values generated in your analysis in QuPath.