wsireg and napari-wsireg workshop for i2k conference
This workshop will introduce wsireg and napari-wsireg to participants and demonstrate how to use wsireg to register whole slide images in complex experimental designs. wsireg permits configuring complex registration in a graph where nodes are images, and edges are transformations between images. It has many features that aid researchers such as handling point transforms, writing registered, pyramidal whole slide images compatible with QuPath and other popular WSI software.
wsireg:
https://github.com/nhpatterson/wsireg
napari-wsireg:
https://github.com/nhpatterson/napari...
napari:
https://github.com/napari
i2k conference:
https://www.i2kconference.org/
0:00 Introduction
1:10 Installation/starting napari
4:34 Background
11:04 Concept: Images/modalities
12:56 Concept: Registration graph
13:46 Demo: Adding image modalities
17:17 Concept: Image preprocessing for registration
20:34 Demo: Setting up image preprocessing
25:56 Concept: Registration paths
26:30 Demo: Setting up registration paths (2 images)
28:46 Concept: Project name and output directory
30:23 Demo: Setting project name and output (2 images)
32:40 Concept: Running/queuing graphs in napari-wsireg
34:29 Demo: Running/queuing graphs
36:48 Concept: Registration graph (direct/indirect registration)
38:38 Concept: 6 image example background information
40:13 Demo: Set up and output of 6 image example
53:10 Concept: Attachment images
54:03 Demo: Adding attachment images
55:44 Concept: Attachment shapes
56:48 Demo: Adding attachment shapes
58:11 Concept: Masks for registration
1:00:00 Demo: Adding and using a mask
1:01:00 Outputs: images, transforms, shapes
1:07:59 Demo: QuPath and wsireg
1:08:49 Concept: Merging modalities after registration
1:10:12 Demo: Adding merge modalities and merge outputs
1:12:40 Demo: Merge modalities in QuPath
1:13:35 Conclusions