Comments (4)
Hello skim245,
Can you share your raw image, mask.mat file from VNS function and nuclei.mat from refineVNS function.
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Hi @madhavitippani
I've uploaded three files in google drive and below is the link!
https://drive.google.com/drive/folders/1zNLtGC0MujHsqYiEZNXL_2LnHbd51FZT?usp=sharing
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Requested access
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There are a couple of things you need to change in the code for your images.
- in the VNS script that is located here
~/VistoSeg/code/VNS.m
comment out line 11 and change line 12 as following
%Img1_smooth = imgaussfilt(Img1,4); %smooth image
he = imadjust(Img1, [.2 .3 0; .6 .7 1],[]); %adjust contrast in image
because smoothening is not working for your images, and you need contrast adjustment on the raw image itself
- in refineVNS script here
~/VistoSeg/code/refineVNS.m
add the following line after line 19
mask_dark_blue = bwareafilt(mask_dark_blue,[5 2000]);
in this line [5 2000] is the size threshold on segmented nuclei. Meaning nuclei with less than 5-pixel area and greater than 2000-pixel area are dropped from the segmentation.
With these changes, I was able to get the following results
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Related Issues (20)
- Explain Visium and/or the data used in this documentation
- Explain how to download the data used in this documentation HOT 2
- Citation information and software name
- Add software requirements
- Avoid full paths
- Be more verbose and describe code chunks HOT 1
- Write a short paper about your software
- OSTA vs the documentation in this repo
- bookdown info
- Reviews are back HOT 2
- image requirements HOT 1
- update refineVNS() to provide csv with shape and size metrics HOT 1
- create thresholding function based on refineVNS() metric.csv output
- update countSpots() function to count nuclei/spot based on centroid of nuclei HOT 1
- Getting cropped spot images HOT 1
- Update citation information HOT 1
- Clarify the docs due to differences between Visium and Visium SPG processing pipeline steps HOT 2
- Error while running the corrected countSpots_centroid.m code HOT 1
- splitSlide show error messages
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