omnipose

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GPU memory usage

2

We have nvidia GPU with 12G memory. If I allocate less than 3 GPUs to run the example mono_channel_3D,ipynb, I got GPU out of memory error. From nvidia-smi, I can...

sunyi000

Question about parallel computing on GPU

3

I have two GPUs on our server. But when I run the model, the second GPU always does not work. I know my job is not very big, so that...

Johnxiaoming

3D training with ValueError(msg)

7

Hi @kevinjohncutler, I'm trying to train a new model using your new 3D implementation, but I'm having the follow error: `python -m omnipose --train --use_gpu --dir ./omni/omnipose_training --mask_filter _masks --n_epochs...

mccruz07

Problem using GPU

2

Hi, I've been trying to use Omnipose with GPU for two days. Actually, Cellpose works like charm, but when I try to use Omnipose I always get this error: RuntimeError:...

koopa31

Unable to evaluate 3D unet in CLI

2

Hello! I am trying to evaluate the 3D UNet on a plant segmentation datasets via the CLI with this command: https://github.com/security `python -m omnipose --omni --dir ./ --dim 3 --z_axis...

buswinka

peakdetect 1.2 causes dependency conflict

3

Looks like peakdetect that you use depends on super-outdated scipy, for this reason I get: ``` from scipy import fft, ifft ImportError: cannot import name 'ifft' from 'scipy' (/home/antonkulaga/.local/lib/python3.10/site-packages/scipy/__init__.py) ```...

antonkulaga

Thanks for your great work! While I tried to get the unique contour by calling the function **omnipose.core.get_contour()**, I got contour missing. ``` python contour_map, contour_list, unique_L = omnipose.core.get_contour(msk, affinity_graph,...

WuJunxu

Segmenting 3D Tiff with plantomni: RuntimeError: Expected output.numel() <= std::numeric_limits::max() to be true, but got false.

2

I have a mono channel 3D tiff file that I read into an array of shape (151, 1608, 1608). this corresponds to (zstack, height, width). i'm trying to segment nuclei...

mrdandelion6

3D Segmentation with Omnipose using 2D Cellpose models

1

I am trying to segment 3D tiff cell images with Omnipose but am running into a shape mismatch error. I am following the example code on the [Omnipose documentation](https://omnipose.readthedocs.io/examples/mono_channel_3D.html) and...

mrdandelion6

Train an Omnipose model with 3-channel input images

1

Hi all, I am trying to train a model from scratch with: - Input images: (160,160,3) RGB images (array of uint8) - Input masks: (160,160) 16-bit images - Training via...

ThaoCao