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I can't Run Lois to ROI on my image. #22
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Hi!
The problem is that you were trying to segment and RGB image and not a
grayscale 8 bit image.
If you open your original image in ImageJ, go to Image / Type / 8-bit and
save it in that format, you can run the Cellpose Colab and it should work.
I attach the label image after running the colab with the grayscale image. (just for visualization, I color coded the
labels using MorpholibJ label images plugin in ImageJ), but this is just a
visualization tool, it works the same as the output image from the colab.
![Snap01-c1_label with color code](https://github.com/ariel-waisman/LabelsToROIs/assets/20975344/ec94f2cb-10e8-4c71-9fc4-77fdbcca3edb)
And this is an overlay of the ROIs and your original image.
![Snap01-c1-1 overlay](https://github.com/ariel-waisman/LabelsToROIs/assets/20975344/2febeaaa-df6f-41d2-98c9-d90be26a563e)
Hope that helps!
Good luck,
Ariel
…On Fri, Jul 5, 2024 at 9:51 AM Momo-MLB ***@***.***> wrote:
Greeting,
I would love to use this amazing tool LOIStoROI to segment and quantify
sections of myofiber. I followed the steps one by one (cellpose and Lois to
Roi plugin on Fiji, both on windows and on mac) but it doesn't work.
First : the label png image that I got from cellpose was just a black
image : is that normal ? (I don't know how should the image look like). I
attach herein the two images, the original and the label output image.
Second, (I assumed the black label image is normal so I proceed to the
Lois to Roi plugin on Fiji (updated to the last version). I choose single
image, and load the original TIF and the label image PNG. when I click GO
two windows appear but they are blank nothing is going on (I tried again
and again but invane, I also wated two hours, thought maybe it's a
processor thing but also invane). When I tried that on windows, the Fiji
app closes abruptly when I click on GO.
Please help me resolve this issue please.
Thank you all in advance !!!!!
Here is the label image i got from the Colab-Cellpose
Snap01-c1_label.png (view on web)
<https://github.com/ariel-waisman/LabelsToROIs/assets/174803747/62e618ee-9270-44b6-b6ee-5ef360edd676>
and I converted the TIF image to JPEG so I can upload it here.
Snap01-c1.jpeg (view on web)
<https://github.com/ariel-waisman/LabelsToROIs/assets/174803747/63ce53d2-ae4c-4330-b72f-45b11c46fcb0>
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Greetings DOCTOR !!!!! THANK YOU SOOOOOOOO MUCH THANK YOUUUU SO MUCH !!! It worked THANK YOUUUU SO MUCH , you saved hours of my times THANK YOUUUUUUU SO MUCH DOCTOR Ariel. WISH YOU ALL THE BEST ! |
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Greeting,
I would love to use this amazing tool LOIStoROI to segment and quantify sections of myofiber. I followed the steps one by one (cellpose and Lois to Roi plugin on Fiji, both on windows and on mac) but it doesn't work.
First : the label png image that I got from cellpose was just a black image : is that normal ? (I don't know how should the image look like). I attach herein the two images, the original and the label output image.
Second, (I assumed the black label image is normal so I proceed to the Lois to Roi plugin on Fiji (updated to the last version). I choose single image, and load the original TIF and the label image PNG. when I click GO two windows appear but they are blank nothing is going on (I tried again and again but invane, I also wated two hours, thought maybe it's a processor thing but also invane). When I tried that on windows, the Fiji app closes abruptly when I click on GO.
Please help me resolve this issue please.
![Snap01-c1_label](https://private-user-images.githubusercontent.com/174803747/346127276-62e618ee-9270-44b6-b6ee-5ef360edd676.png?jwt=eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJpc3MiOiJnaXRodWIuY29tIiwiYXVkIjoicmF3LmdpdGh1YnVzZXJjb250ZW50LmNvbSIsImtleSI6ImtleTUiLCJleHAiOjE3MjQwNTcxMjksIm5iZiI6MTcyNDA1NjgyOSwicGF0aCI6Ii8xNzQ4MDM3NDcvMzQ2MTI3Mjc2LTYyZTYxOGVlLTkyNzAtNDRiNi1iNmVlLTVlZjM2MGVkZDY3Ni5wbmc_WC1BbXotQWxnb3JpdGhtPUFXUzQtSE1BQy1TSEEyNTYmWC1BbXotQ3JlZGVudGlhbD1BS0lBVkNPRFlMU0E1M1BRSzRaQSUyRjIwMjQwODE5JTJGdXMtZWFzdC0xJTJGczMlMkZhd3M0X3JlcXVlc3QmWC1BbXotRGF0ZT0yMDI0MDgxOVQwODQwMjlaJlgtQW16LUV4cGlyZXM9MzAwJlgtQW16LVNpZ25hdHVyZT1lMmU0ODE5YjhhYmM3MzAyYjYxZmRmMGZmNGFlN2VlY2M3NmVkN2UzMjQwNzI2ZWQ0ZjJkNzAyNmQ2NWJhZjEwJlgtQW16LVNpZ25lZEhlYWRlcnM9aG9zdCZhY3Rvcl9pZD0wJmtleV9pZD0wJnJlcG9faWQ9MCJ9.gHa6nM-oTy6ygRHq1LhSoDEj04V6WP_0DTN-UagaBfU)
![Snap01-c1](https://private-user-images.githubusercontent.com/174803747/346127704-63ce53d2-ae4c-4330-b72f-45b11c46fcb0.jpeg?jwt=eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.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.aLwKAY6ZkgktaTlr2zmkGK12l9llt-yBzXiZ0ASeZQQ)
Thank you all in advance !!!!!
Here is the label image i got from the Colab-Cellpose
and I converted the TIF image to JPEG so I can upload it here.
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