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This document aims to compile the documents that were created during the QuPath Workshop and Hackathon which took place from April 17th till April 20th = Questions & Answers = == Is it possible to open confocal images (lsm files)? == Yes. But you'll need the QuPath BioFormats Extension, which you'll need to install [[ https://github.com/qupath/qupath-bioformats-extension | according to the instructions on GitHub ]] == Can there be more than 2 stains? == are z-stacks supported? are bit depths other than 8-bit supported? can a custom version of ImageJ (e.g. FIJI) be used instead of the one shipped with QuPath can the macro runner run imageJ macros (.ijm) only or also scripts written in a different language? Can we set a different threshold of cell detection in a specific area ? cell detection behaviour on fluorescence images Would it be possible to duplicate an annotation from one z plane to another z plane in the same image? How many channels are supported by QuPAth for the confocal image? I have 4 channels, I can modify brightness/contrast for all of them however cell detection and measurements are possible only with 3 channels and not with 4th one. Does changing brightness/contrast affect measured values? Is there a batch mode? can we measure inside the overlay that was sent from imageJ? Can we do pixel classification? What other objects besides cells can be classified? Can there be different staining definitions for the cell detection? Set Image Type as “Other” -> Can define Stain Vectors by annotation Can we have more than 2 stains? Can we make an annotation out of a classification result? How do I set the resolution of an image manually? is there a way to make “close project” also close the currently open image? Is it possible to add measurements to regions from ImageJ? See this Blog Post How do we detect other things like fibers or differently shaped cells?

This document aims to compile the documents that were created during the QuPath Workshop and Hackathon which took place from April 17th till April 20th = Questions & Answers = == Is it possible to open confocal images (lsm files)? == Yes. But you'll need the QuPath BioFormats Extension, which you'll need to install [[ https://github.com/qupath/qupath-bioformats-extension | according to the instructions on GitHub ]] == Can there be more than 2 stains? == The current color deconvolution can technically work with 3 stains. This however will be the future job of the pixel classification extension. To try it with different stains, you need to set the Image Type to **Brigthfield (Other)** under the Image Tab. You will need to estimate the stain vectors using ImageJ's Color Deconvolution plugin and enter them manually. Otherwise you can create a **Recangular Annotation** and then double click on the Stain # value you want to set. Careful to choose regions that have a "pure" component. == Are Z-Stacks supported? == Yes, QuPath can read Z Stacks as well as time series. It will not, however, perform 3D detections and does not support 3D annotations == Are bit depths other than 8-bit supported? == Yes, but the support is currently limited, as QuPath was originally meant to work on RGB images only. The capacity top open images other than 8-bit will depend on the image reader, and currently it is possible with BioFormats, but not ideal. Expect improved support in the future. == Can a custom version of ImageJ (e.g. FIJI) be used instead of the one shipped with QuPath == Like ICY, QuPath runs its own instance of ImageJ. You could replace the JAR files with other 'simple' ImageJ flavors, but Fiji, which contains both ImageJ1 and ImageJ2 is currently too contrived to be supported. The **suggested** way to use and extend the ImageJ functionality is to point QuPath to your current ImageJ's plugins folder. Any dependencies would have to be in the `jars` folder of QuPAth. == Can the macro runner run ImageJ macros (.ijm) only or also scripts written in a different language? == Currently the Macro Runner only runs ImageJ1 macros. == Can we set a different threshold of cell detection in a specific area ? == Yes, but through a script. To make it work, you would define different classes for your annotations. then going through them, for each annotation you would launch a new 'cell detection' based on the class. == What is the Cell Detection behaviour on fluorescence images? == If the image type is set to Fluorescence (from the Image tab), Cell detection will ask for the channel to use for detecting and offer identical parameters as for brightfield. The only difference will usually be in the value of the threshold, which will typically be higher than the one used for Brigthfield. NOTE: The Positive Cell Detection extension will **not** allow you to select the threshold on another channel to classify your detections. You can currently do this through a script though. === Example Script === ```lang=java // Set the cells with an average nuclear intensity on channel 3 above 40 as positive setCellIntensityClassifications("Nucleus: Channel 3 mean",40) // The name of the measurement corresponds to the column name in Measure > Show Detection Measurements ``` == Would it be possible to duplicate an annotation from one z plane to another z plane in the same image? == It is rather contrived but we have a script for that ```lang=java import qupath.imagej.objects.ROIConverterIJ import qupath.lib.objects.PathAnnotationObject import qupath.lib.roi.PathROIToolsAwt import qupath.lib.scripting.QPEx // Change Z for currently selected annotation // Choose the new Z position it will have def newZ = 2 // Get def imageData = QPEx.getCurrentImageData() def pathObject = imageData.getHierarchy().getSelectionModel().getSelectedObject() def roi = pathObject.getROI() def shape = PathROIToolsAwt.getShape(roi) def roi2 = PathROIToolsAwt.getShapeROI(shape, -1, 1, roi.getT(), 0.5) def annotation = new PathAnnotationObject(roi2) imageData.getHierarchy().addPathObject(annotation, false) ``` How many channels are supported by QuPAth for the confocal image? I have 4 channels, I can modify brightness/contrast for all of them however cell detection and measurements are possible only with 3 channels and not with 4th one. Does changing brightness/contrast affect measured values? Is there a batch mode? can we measure inside the overlay that was sent from imageJ? Can we do pixel classification? What other objects besides cells can be classified? Can there be different staining definitions for the cell detection? Set Image Type as “Other” -> Can define Stain Vectors by annotation Can we have more than 2 stains? Canwe make an annotation out of a classification result? Ho do I set the resolution of an image manually? is there a way to make “close project” also close the currently open image? Is it possible to add measurements to regions from ImageJ? See this Blog Post How do we detect other things like fibers or differently shaped cells?

This document aims to compile the documents that were created during the QuPath Workshop and Hackathon which took place from April 17th till April 20th = Questions & Answers = == Is it possible to open confocal images (lsm files)? == Yes. But you'll need the QuPath BioFormats Extension, which you'll need to install [[ https://github.com/qupath/qupath-bioformats-extension | according to the instructions on GitHub ]] == Can there be more than 2 stains? == The current color deconvolution can technically work with 3 stains. This however will be the future job of the pixel classification extension. To try it with different stains, you need to set the Image Type to **Brigthfield (Other)** under the Image Tab. You will need to estimate the stain vectors using ImageJ's Color Deconvolution plugin and enter them manually. Otherwise you can create a **Recangular Annotation** and then double click on the Stain # value you want to set. Careful to choose regions that have a "pure" component. == Are Z-Stacks supported? == Yes, QuPath can read Z Stacks as well as time series. It will not, however, perform 3D detections and does not support 3D annotations == Are bit depths other than 8-bit supported? == Yes, but the support is currently limited, as QuPath was originally meant to work on RGB images only. The capacity top open images other than 8-bit will depend on the image reader, and currently it is possible with BioFormats, but not ideal. Expect improved support in the future. == Can a custom version of ImageJ (e.g. FIJI) be used instead of the one shipped with QuPath == Like ICY, QuPath runs its own instance of ImageJ. You could replace the JAR files with other 'simple' ImageJ flavors, but Fiji, which contains both ImageJ1 and ImageJ2 is currently too contrived to be supported. The **suggested** way to use and extend the ImageJ functionality is to point QuPath to your current ImageJ's plugins folder. Any dependencies would have to be in the `jars` folder of QuPAth. == Can the macro runner run ImageJ macros (.ijm) only or also scripts written in a different language? == Currently the Macro Runner only runs ImageJ1 macros. == Can we set a different threshold of cell detection in a specific area ? == Yes, but through a script. To make it work, you would define different classes for your annotations. then going through them, for each annotation you would launch a new 'cell detection' based on the class. are z-stacks supported?== What is the Cell Detection behaviour on fluorescence images? == are bit depths other than 8-bit supported?If the image type is set to Fluorescence (from the Image tab), Cell detection will ask for the channel to use for detecting and offer identical parameters as for brightfield. The only difference will usually be in the value of the threshold, which will typically be higher than the one used for Brigthfield. can a custom version of ImageJ (e.g.NOTE: The Positive Cell Detection extension will **not** allow you to select the threshold on another channel to classify your detections. You can currently do this through a script though. === Example Script === ```lang=java // Set the cells with an average nuclear intensity on channel 3 above 40 as positive setCellIntensityClassifications("Nucleus: Channel 3 mean",40) // The name of the measurement corresponds to the column name in Measure > Show Detection Measurements ``` == Would it be possible to duplicate an annotation from one z plane to another z plane in the same image? FIJI) be used instead of the one shipped with QuPath== It is rather contrived but we have a script for that ```lang=java import qupath.imagej.objects.ROIConverterIJ import qupath.lib.objects.PathAnnotationObject import qupath.lib.roi.PathROIToolsAwt import qupath.lib.scripting.QPEx // Change Z for currently selected annotation // Choose the new Z position it will have can the macro runner run imageJ macros (.ijm) only or also scripts written in a different language?def newZ = 2 // Get def imageData = QPEx.getCurrentImageData() def pathObject = imageData.getHierarchy().getSelectionModel().getSelectedObject() Can we set a different threshold of cell detection in a specific area ?def roi = pathObject.getROI() cell detection behaviour on fluorescence imagesdef shape = PathROIToolsAwt.getShape(roi) Would it be possible to duplicate an annotation from one z plane to another z plane in the same image?def roi2 = PathROIToolsAwt.getShapeROI(shape, -1, 1, roi.getT(), 0.5) def annotation = new PathAnnotationObject(roi2) imageData.getHierarchy().addPathObject(annotation, false) ``` How many channels are supported by QuPAth for the confocal image? I have 4 channels, I can modify brightness/contrast for all of them however cell detection and measurements are possible only with 3 channels and not with 4th one. Does changing brightness/contrast affect measured values? Is there a batch mode? can we measure inside the overlay that was sent from imageJ? Can we do pixel classification? What other objects besides cells can be classified? Can there be different staining definitions for the cell detection? Set Image Type as “Other” -> Can define Stain Vectors by annotation Can we have more than 2 stains? Can we make an annotation out of a classification result? How do I set the resolution of an image manually? is there a way to make “close project” also close the currently open image? Is it possible to add measurements to regions from ImageJ? See this Blog Post How do we detect other things like fibers or differently shaped cells?