-
Hi, I was wondering if you have a workflow for analyzing IMC data using python (or more specifically, the AnnData-Scanpy-Squidpy ecosystem as mentioned in your preprint [10.1101/2021.11.12.468357](htt…
-
You are right, the check on `c_coords` should be one the output data. I merged already because I need to merge #594, which was opened against the current PR. Please can you make a patch for fixing tha…
giovp updated
2 weeks ago
-
## Description
After loading a single FOV (CosMx data), which was saved to h5ad with a sparse X, I noticed the memory required was 13GB(!). Investigating with `pymplr.asizeof()` revealed that:
>…
-
Hi I am on scanpy=1.9.3 squidpy=1.2.3 tangram=1.0.4 torch=1.13.1+cu117
I am trying to integrate single cell and merfish data.
A marker list of 104 genes was correctly prepared and I have verifie…
-
Thank you for making a very interesting tool.
I've been working through the tutorial and noticed that the datasets already include segmentation masks. Can you provide advice on how to create masks …
-
Hi there
I am trying to run umap and i get the error: module 'umap' has no attribute '__version__'
I have tried uninstalling and reinstalling umap-learn
however this hasn't worked - would anyone …
-
Hi,
for ehrapy we need the ability to move values from X to obs/var/obsm/varm and the other way around. Quoting myself:
> Would be very useful to have a method to move data from X to obs and the…
-
Hi,
I specified `segmented_custom` in the following code
```
sq.im.segment(img=img2, layer="image_smooth", channel=None, method=cellpose_he, channel_cellpose=0, flow_threshold=1)
…
WT215 updated
2 weeks ago
-
Hi,
Just discovered this really cool package!
I have a question regarding the implementation of Ripleys statistics. What I am interested in is computing e.g. Ripley's K for n subsets of points tha…
giovp updated
2 years ago
-
## Description
When the `groups`parameter is specified in `sq.pl.spatial_segment` the cells that are plotted are not the cells where `adata.obs[color].isin(groups)`. For example with the `mibitof` …