qupath/qupath-docs

QuPath documentation

qupath-docs's Issues

Document need for layout with TensorFlow/StarDist models in v0.5.0

See https://forum.image.sc/t/qupath-v-0-5-tensorflow-issue/89908/2

Update link to jdk download source

I just noticed that the archive page cited in the build reference (https://adoptopenjdk.net/) has moved to a different page:

The new link is https://adoptium.net/temurin/releases

GeoJSON export, in the most recent version?

Hi, quick question (and thanks for making some really great software).
I saw that GeoJSON export has recently been added to the docs but on my current version, 0.2.3 on mac (which I think is the most recent), I have no Object data… option under File.

So I also tried the script export but it seems that the function does not exist -

def annotations = getAnnotationObjects()
def path = "/Users/ca/Desktop/file.geojson"

// 'FEATURE_COLLECTION' is standard GeoJSON format for multiple objects
exportObjectsToGeoJson(annotations, path, "FEATURE_COLLECTION")

ERROR: MissingMethodException at line 5: No signature of method: org.codehaus.groovy.jsr223.GroovyScriptEngineImpl.exportObjectsToGeoJson() is applicable for argument types: (ArrayList, String, String) values: [[Annotation (Polygon) (Tumor)], ./file.geojson, FEATURE_COLLECTION]

Am I just running an old version without realising it or is it going to be rolled out in the next release? Cheers

Typo in documentation

qupath-docs/docs/tutorials/density_maps.md

Line 199 in a7af49a

- **Density peaks only** -- In theory, one might expect a hotspot to be a 'peak' in the density map, where the density is higher than in surrounding pixels. In practice, the mighest density within any region might not be a peak (because the peak is outside the region). On the other hand, removing the peak criterion could result in multiple hotspots being generated within a single large, high-density region. This option allows you to toggle whether a peak criterion is used or not.

should say "highest" not "mighest"

Sample scripts out of date for v0.5.0

See https://www.youtube.com/watch?v=Ou5qqHK5NV8

Specifically the Dialogs class has moved!

Add license info (& ReadMe)

A recent forum topic reminds me that these docs should have an explicit license statement.

I thought they did, but I can't find it either.

For all original content, I propose using CC-BY 4.0 and adding a statement to that effect to the Acknowledgements page. Where screenshots are derived from images using different licenses, reuse might also require referencing them - if so, that info should also be on the acknowledgements page.

From the Contributors I see that the only other people who have committed to the docs are

• @melvingelbard
• @dkurt
• @zindy
• @astrojuanlu

If any of you have opinions on this (or prefer your commits excluded if moving to CC-BY) please let me know - otherwise I'll make the changes sometime early in the new year.

Thanks!

typos in scripting section

Hi, I just noticed two errors when browsing the documentation in this section: https://qupath.readthedocs.io/en/latest/docs/scripting/overview.html#working-with-bufferedimages

• First code block is not closed properly (indentation issue)
• BufferedImage.TYPE*BYTE*GRAY should instead be BufferedImage.TYPE_BYTE_GRAY

Fix v0.4 references in WSInfer docs

e.g. see

qupath-docs/docs/deep/wsinfer.md

Lines 13 to 18 in 132a842

	## Requirements
	- QuPath [version 0.4](https://qupath.github.io/) (installation instructions [here](https://qupath.readthedocs.io/en/0.4/docs/intro/installation.html)).
	- At least one whole slide image
	- [WSInfer QuPath Extension](https://github.com/qupath/qupath-extension-wsinfer/releases)
	- PyTorch (this can be downloaded while using the extension)

Should update for v0.5, with benchmarks as described at

• #89

benchmarking qupath-wsinfer

i am using this issue to provide info on the data i use when benchmarking wsinfer in qupath.

image: TCGA-3C-AALI-01Z-00-DX1.F6E9A5DF-D8FB-45CF-B4BD-C6B76294C291.svs (link to image for download on Genomic Data Commons)

geojson representation of the square region. the region has an area of 100 millimeters squared. (the geojson coordinates are in pixels, and it is the equivalent of 100 mm2 in the whole slide image).

i will update this issue with my running times for a 12th gen i5 cpu and an nvidia 2080ti gpu, both in windows 11.

here are running times.... on an i5-12600K, it took 6 minutes 37 seconds. on an NVIDIA RTX 2080Ti, it took 40 seconds. please see other environment details below. this was using the WSI and ROI in this issue.

• os: windows 11
• qupath v0.4.4
• wsinfer extension v0.2.1
• model "breast-tumor-resnet34.tcga-brca"
• ROI of 100 mm^2 (see geojson below)
• openslide loader (i think -- i'm not sure how to change this to bioformats)

{
  "type": "FeatureCollection",
  "features": [
    {
      "type": "Feature",
      "id": "9724d4e3-cd6d-4630-a474-4d71e35db065",
      "geometry": {
        "type": "Polygon",
        "coordinates": [
          [
            [
              25471,
              25869
            ],
            [
              65471,
              25869
            ],
            [
              65471,
              65869
            ],
            [
              25471,
              65869
            ],
            [
              25471,
              25869
            ]
          ]
        ]
      },
      "properties": {
        "objectType": "annotation"
      }
    }
  ]
}

here is a groovy script i was using to measure the runtime:

import groovy.time.TimeCategory

// Set device (cpu, gpu, or mps)
qupath.ext.wsinfer.ui.WSInferPrefs.deviceProperty().setValue("gpu");
// Set number of parallel workers
qupath.ext.wsinfer.ui.WSInferPrefs.numWorkersProperty().setValue(8);

// ---
selectAnnotations()
def timeStart = new Date()
qupath.ext.wsinfer.WSInfer.runInference("kaczmarj/breast-tumor-resnet34.tcga-brca")
def timeStop = new Date()
duration = TimeCategory.minus(timeStop, timeStart)
println duration

Add a section about building and modifying the read-the-docs documentation locally?

I'm not very well versed in building Sphinx and read-the-docs documentation, and struggled a bit with creating a local environment.

I ended up using the make script make html and pip install all the missing modules, then sphinx-serve.

Edit: The package sphinx-autobuild suggested by Pete below is much better than the one I suggested and is being actively maintenained. It will automatically reload the page in a browser when changes the source file is saved.

I could start a pull request and describe how I got my environment to work, if you'd like?

Add multi-viewer feature

Add a mention/page about the multi-viewer feature.

Provide an example script for exporting images as an OME-TIFF

Currently, the Exporting images page doesn't have a demo for how to export images loaded into QuPath as a .ome.tif. While the Tile Exporter section does support this, some users may want to export whole images, especially if they were aligned and concatenated into a sparse image. Maybe something like this: https://forum.image.sc/t/batch-convert-dicom-to-tiff-files/87987/4?u=mark_zaidi

Add a section about vscode?

Hello,

this is something I'm working on: I've been using VSCode quite a lot to develop and debug QuPath, on Windows, Linux and more recently MacOSX.

I think I could write a section about how to do this if it helps bringing in people. I haven't been able to push to my github just quite yet, but I think this will be trivial to sort.

So:

• where to get vscode and what Extensions are needed
• where to download the JAVA JDK from (I use Microsoft's build)
• Git clone, add a .vscode config
• Initial Gradle build using the "command line arguments" button
• Debugging QuPath, hotswapping code (I'm a very very basic user of this)
• Git commit / Git push

If there are any expert users, I would happily accept any other useful tidbits!

Cheers,
Egor