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icbm-iupui / volumetric-tissue-exploration-analysis

3D TISSUE CYTOMETRY PLUGIN FOR IMAGEJ DOWNLOAD and INSTALL:
http://imagej.net/VTEA
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Importing segmentation results from other sources. #56

Closed matfallet closed 2 years ago

matfallet commented 4 years ago

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winfrees commented 4 years ago

Sorry for the delay. The current climate is stretching resources! Thank you for your interest in VTEA. Right now VTEA is designed to segment, generate objects internally, measures and then provides the scatter interface. If I understand correctly, you'd like to import ROIs (imagej?) and a set of measurements also from imageJ and use the gating and mapping back interface? Cheers. Thanks for the interest.

matfallet commented 4 years ago

Dear Seth,

Yes that is exact, I am not interested by the segmentation only by the scatterplot and visulaisation back to the image.

Is there a way to implement thsi part in your program, do you want my roi.zip and my image to try ?

Thanks,

Mathieu Fallet

De : Seth Winfree notifications@github.com Envoyé : mardi 28 avril 2020 03:15:44 À : icbm-iupui/volumetric-tissue-exploration-analysis Cc : Mathieu FALLET; Author Objet : Re: [icbm-iupui/volumetric-tissue-exploration-analysis] Dear developper, I am very interested by your project. I would like to test it, do you have any documentation ? For example, I have an image with ROI.zip and measurents(ID, mean cell type 1, mean ...

Sorry for the delay. The current climate is stretching resources! Thank you for your interest in VTEA. Right now VTEA is designed to segment, generate objects internally, measures and then provides the scatter interface. If I understand correctly, you'd like to import ROIs (imagej?) and a set of measurements also from imageJ and use the gating and mapping back interface? Cheers. Thanks for the interest.

- You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/icbm-iupui/volumetric-tissue-exploration-analysis/issues/56#issuecomment-620319340, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AJ4PCC5ZI2GTSIOWBSEZPZ3ROYU4BANCNFSM4MJMDQ2Q.

icbm-iupui commented 4 years ago

Mathieu,

?

There are a number of entry points/methods we could use. The simplest would probably be to write an import class that interacts with "MicroExplorer" (https://github.com/icbm-iupui/volumetric-tissue-exploration-analysis/blob/master/src/main/java/vteaexploration/MicroExplorer.java). I'd probably convert the existing import class structure to a more generalizable approach and move from there. I'm going to combine your request (#56) with another (#57 ) and start working through the implementation.

Thanks again for your interest,

Seth

winfrees commented 4 years ago

To summarize we'd like to implement importing of segmentation results from other sources into the MicroExplorer functionality:

1)import segmentation from Integer images with or without repeating indices (8,16,32 bit, re #57 ) 2)import ROI based segmentations (imageJ, etc) 3)import existing measurements keyed to indices (must be unique, re #57 ) 4)import images for mapping and measurements 5)perform measurements on imported images using these segmentations

matfallet commented 4 years ago

ok great, we are working on the same subject using R but would be great to have a plugin that we can use in Image J that can make live scatterplot and look directly the dots in the scatterplots on ROI in the image.

Best, Mathieu

De : Seth Winfree notifications@github.com Envoyé : samedi 2 mai 2020 16:49:12 À : icbm-iupui/volumetric-tissue-exploration-analysis Cc : Mathieu FALLET; Author Objet : Re: [icbm-iupui/volumetric-tissue-exploration-analysis] Importing segmentation results from other sources. (#56)

To summarize we'd like to implement importing of segmentation results from other sources into the MicroExplorer functionality:

1)import segmentation from Integer images with or without repeating indices (8,16,32 bit, re #57https://github.com/icbm-iupui/volumetric-tissue-exploration-analysis/issues/57 ) 2)import ROI based segmentations (imageJ, etc) 2)import existing measurements keyed to indices (must be unique, re #57https://github.com/icbm-iupui/volumetric-tissue-exploration-analysis/issues/57 ) 3)perform measurements on imported segmentations

- You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/icbm-iupui/volumetric-tissue-exploration-analysis/issues/56#issuecomment-622965388, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AJ4PCC3I5JORAARM6HOL2UDRPQXGRANCNFSM4MJMDQ2Q.

winfrees commented 4 years ago

The import of ImageJ Rois (via an embedded RoiManager) is now possible in the VTEA workflow. This is a partial completion of this issue/feature request. Reference: see 15373b6 in the RengLUT branch.
RoiBasedSegmentation_092320

winfrees commented 4 years ago

Recap and status on issues:

1)import segmentation from Integer images with or without repeating indices (8,16,32 bit, re #57 ) in-progress 2)import ROI based segmentations (imageJ, etc) completed This is for ImageJ1 Rois. Looking into ImageJ2/imglib2 and cellprofiler 3)import existing measurements keyed to indices (must be unique, re #57 ) completed This has been done for awhile, use the import CSV button on the Explorer window 4)import images for mapping and measurements queued 5)perform measurements on imported images using these segmentations in-progress

winfrees commented 4 years ago

Finalized import of segmented nuclei from a segmentation map as indicated in 3da0ef5. This may fail for unusually large objects but is functional for fields of nuclei at 20-30x. These exceptions will be handled in a future change.

winfrees commented 4 years ago

Recap and status on issues:

1)import segmentation from Integer images with or without repeating indices (8,16,32 bit, re #57 ) completed 2)import ROI based segmentations (imageJ, etc) completed This is for ImageJ1 Rois. Looking into ImageJ2/imglib2 and cellprofiler 3)import existing measurements keyed to indices (must be unique, re #57 ) completed This has been done for awhile, use the import CSV button on the Explorer window 4)import images for mapping and measurements moving to a new issue-this requires mostly gui changes and working with (5) 5)perform measurements on imported images using these segmentations moving to a new issue-this requires the import of image data and passing through the MeasurementProcessor.

Sub-issues 4 and 5 are being moved to issue #59.

winfrees commented 4 years ago

@matfallet , if there is functionality missing to address #57, please let me know. Otherwise I'd like to close this issue.

@schienstockd, the ability to import a segmentation map has been implemented (#56). Let me know if the functionality described in 3da0ef5 addresses this feature request.

schienstockd commented 4 years ago

I'm not sure how this works now. Could you give a small tutorial to your solution?

What I have is an image called "seg" which is a 32-bit TIF where each segmented objects has a unique ID. The intensities are then taken from a multi-channel image called "raw".

Is that possible to combine with this?

winfrees commented 2 years ago

These functionality have been implemented. A demonstration will be presented here within the next week.