cellpose
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MouseLand
a generalist algorithm for cellular segmentation with human-in-the-loop capabilities
When using make_train.py to generate three different slice-views of input image volumes, which settings do you recommend for nimg_per_tif? For instance, say you have anisotropic volumes of shape 34 *...
**Is your feature request related to a problem? Please describe.** I'm working with large, heterogeneous tissue images (e.g., tumor samples) where cell sizes vary significantly across regions. The current global...
Hi, I’m fine-tuning Cellpose SAM and have two questions: 1. **Color/intensity augmentations** The paper states that, during training, images undergo: * 25% contrast inversion (`x → 1 − x`) *...
In CLI mode, when using 4D images, the image is always opened with `io.imread_3D` when `channel_axis` has a truthy value. The result is an unwanted swap between the last axis...
I think there is a sematic error in the learning objective loss function. in the train_seg function, at the part where you would compute mse between predicted flows and Gt...
it is running well on A100, but when I run it on B200, it throw a exception below. I search about this, not sure, looks like Cellpose's GPU acceleration module...
On XY projections, mask outlines fully enclose the mask with a white-grey line, but in XZ and YZ projections the outlines appear fragmented. I haven’t tried exporting the masks, so...
Here is a small bug just let you know. Cellpose3 GUI layout information shows the cellpose2 GUI
Feeding a list of 256x256 grayscale images to .eval ignores the batch_size and defaults to a specific number. I am unable to increase GPU memory utilization by increasing batch_size at...
**Describe the bug** I have trained a Cellpose 4 model on chunks (128*128 px) from brain images. When I apply the model to the full-size images, it generally works well....
