ariel-waisman
commented
2 months ago 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.
And this is an overlay of the ROIs and your original image.
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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Momo-MLB
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
and I converted the TIF image to JPEG so I can upload it here.
