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SydneyBioX / BIDCell

Biologically-informed deep learning for cell segmentation of subcelluar spatial transcriptomics data
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Question about nuclei segmentation #12

Open chenyhvvvv opened 3 months ago

chenyhvvvv commented 3 months ago

When I run through your pipeline, there is always an error of Traceback (most recent call last): File "/import/home2/yhchenmath/Code_raw/BIDCell-main/run.py", line 3, in model.run_pipeline() File "/import/home2/yhchenmath/Code_raw/BIDCell-main/bidcell/BIDCellModel.py", line 40, in run_pipeline self.preprocess() File "/import/home2/yhchenmath/Code_raw/BIDCell-main/bidcell/BIDCellModel.py", line 61, in preprocess segment_nuclei(self.config) File "/import/home2/yhchenmath/Code_raw/BIDCell-main/bidcell/processing/nuclei_segmentation.py", line 120, in segment_nuclei patch_nuclei = segment_dapi(patch_resized, config.nuclei.diameter, config.nuclei.use_cpu) File "/import/home2/yhchenmath/Code_raw/BIDCell-main/bidcell/processing/nuclei_segmentation.py", line 26, in segmentdapi mask, , , = model.eval(img, diameter=diameter, channels=channels) File "/home/yhchenmath/anaconda3/envs/bidcell/lib/python3.10/site-packages/cellpose/models.py", line 188, in eval masks, flows, styles = self.cp.eval(x, channels=channels, File "/home/yhchenmath/anaconda3/envs/bidcell/lib/python3.10/site-packages/cellpose/models.py", line 410, in eval masks, styles, dP, cellprob, p = self._run_cp( File "/home/yhchenmath/anaconda3/envs/bidcell/lib/python3.10/site-packages/cellpose/models.py", line 517, in _run_cp outputs = dynamics.resize_and_compute_masks( File "/home/yhchenmath/anaconda3/envs/bidcell/lib/python3.10/site-packages/cellpose/dynamics.py", line 779, in resize_and_compute_masks mask, p = compute_masks(dP, cellprob, p=p, niter=niter, File "/home/yhchenmath/anaconda3/envs/bidcell/lib/python3.10/site-packages/cellpose/dynamics.py", line 830, in compute_masks mask = get_masks(p, iscell=cp_mask) File "/home/yhchenmath/anaconda3/envs/bidcell/lib/python3.10/site-packages/cellpose/dynamics.py", line 746, in get_masks M0 = M[tuple(pflows)] IndexError: index -2147483628 is out of bounds for axis 0 with size 5140

The dapi file is download directly from the 10x website. What's wrong with it?

xhelenfu commented 3 months ago

Hi, may I know the name/link to the dataset and file name of the DAPI image you are using? I can take a look at this issue

chenyhvvvv commented 3 months ago

Oh. This because the cuda version and I have solved it. And I have a question about the paper Fig.2 (b). Your method uses the cellpose nuclei segmentation result to get the number of batch size. So I wonder why the segmented cell number of BIDCell is larger than the cellpose(nuclei)? And for the Xenium breastcancer1, the segmented cell number of 10X nuclei and the 10X have such a gap? Since in nucleus_boundaries.parquet of the original data both have 160000+ cell id.

chenyhvvvv commented 3 months ago

And can you provide the scRNA reference and Markere gene or tell me how to find them on stereo-seq mouse brain? I wonder if they are from Allen mouse brain too. Thanks a lot!