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PreibischLab / RS-FISH

Tool for precise, interactive, fast and scalable FISH spot detection
GNU General Public License v2.0
45 stars 14 forks source link

Add the detection to the RoiManager #4

Closed romainGuiet closed 3 years ago

romainGuiet commented 3 years ago

Hi @team, Thank you for releasing this tool!

Would it be possible to add an option to the GUI to add the detection to the RoiManager?

An easy workaround is to use the interactive mode and at the histogram step to use "Image>Overlay>To Roi Manager", but it's not compatible with advanced mode (nor batch) Another workaround would be to make a script to go through the result table and make rois from coordinates, but it sounds like re-doing something.

Thank you again,

Best,

R

StephanPreibisch commented 3 years ago

Hi @romainGuiet, I am trying right now. Is there a convenience method for setting a ROI at slice z? It is not clear to me how to set 3D positions, specifically how to add a PointROI for a specific slice. Thanks so much!

StephanPreibisch commented 3 years ago

This does something, but I cannot go through the image and the spots pop up in their respective slices. However, it works to select them in the list. Any help would be great :)

https://github.com/PreibischLab/RadialSymmetryLocalization/commit/bab2883c5544265c6b53aff531aa8a17ae9c2749

Thanks so much!

romainGuiet commented 3 years ago

Hi @StephanPreibisch ,

It is not clear to me how to set 3D positions...

I think it's clear for no one 😏 ! The main issue (to my understanding) is that it behaves differently if the image is a simple stack, or a hyperstack. Please find here a discussion about it.

StephanPreibisch commented 3 years ago

So you think the current version as I wrote it is what users expect? It is already deployed to the update site if you want check ...

romainGuiet commented 3 years ago

I just tested bab2883 (cloned the repo) on the provided multi-dots.tif and I can get the ROIs in the RoiManager!

What I did next was to use "sort" in the RoiManager to have the ROIs ordered by slice (otherwise while reviewing ROIs, from one to another, user jumps in the stack to very different slices).

Would it slow down a lot the processing to add the ROI name (as shown in the RoiManager) to the Results Table ? This might facilitate the review process...

Thank you for the fast implementaion!

romainGuiet commented 3 years ago

So you think the current version as I wrote it is what users expect?

Yes, definetly!

It is already deployed to the update site if you want check ...

Didn't see that coming so fast!

Thanks again