Elyas Heidari

Problem with installing due to the dependency `magick`

5

Hi! apparently there is a new dependency `magick` added. I can not install it on my machine. the usual error: `1: In .inet_warning(msg) :installation of package ‘magick’ had non-zero exit...

not_implemented error trying to add validation step to lightning module

4

### 🐛 Describe the bug Hello esteemed pyg developers, Trying to train the following simple model: ``` class LitSegger(L.LightningModule): def __init__(self, model): super().__init__() self.model = model self.validation_step_outputs = [] def...

error from minimalistic reading of xenium data

2

Hola! just updated both `spatialdata` and `spatialdata-io` trying to read a generic xenium dataset with the following line, I get the error bellow: ``` sdata = spatialdata_io.xenium( 'Xenium_V1_FFPE_Human_Breast_IDC', morphology_mip=False, morphology_focus=False,...

We're are aware that the Seg2Explorer function has bugs. We are working on this issue and will refer to this issue as we solved it. Seg2explorer is a downstream function...

Early stopping for training

1

It was brought to my attention that we have not yet implemented early stopping. This is a reminder for me and @andrewmoorman. - [ ] add early stopping.

> Thank you @senbaikang for your multi-GPU solution!   > > Hi @EliHei2 I realized that the `seg2explorer` function is kind of out-of-date: > https://www.10xgenomics.com/support/software/xenium-onboard-analysis/latest/advanced/xoa-output-zarr > > The `cells.zarr.zip` file cannot...

Xenium Explorer output

2

Hey @EliHei2, thank you for the help! It works now! Regarding the prediction results, I wonder if there is a way to use them as input to xeniumranger's [import-segmentation](https://www.10xgenomics.com/support/software/xenium-ranger/latest/analysis/inputs/segmentation-inputs) command?...

[Bento-tools](https://bento-tools.readthedocs.io/en/latest/) by @ckmah, would be a perfect add-on to segger. It will be beneficial to add it to the validation module. I could thought of the following steps. - [x]...