I attempted to run both the python notebook and bdtnp scripts and encountered some issues with both.
For reconstruct_bdtnp_with_markers.py:
My first commit downsamples cells to 3039 since that appears to be the number present in the current output image: 3039_cells_3039_locations.png. I have replaced this image since it seems like the point sizes are better now. I also kept the updates to results.txt and sdge_3039_cells_3039_locations, although I can drop these if you would prefer.
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For reconstruct_drosophila_embryo_tutorial.ipynb:
My second commit contains numerous fixes to the python notebook, although my output still doesn't appear right. Any advice would be appreciated on producing the last 6 figures of various gene expression in the embryo.
Fixes include:
path names now correctly map to the structure of the repository
subsampling is disabled by default
locations are truncated from (x,y,z) to (x,z) and trimmed to 3039 locations
These changes allow me to run the entire notebook from start to finish without errors, but I still see some issues:
de novo reconstruction images do not appear the same as what is given as an example currently
Do I really need to truncate to 3039 cells because of the number of cells in bdtnp.txt / dge.txt? It only contains 3039 cells, but the initial coords from geometry.txt includes 6078 cells.
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As a computational biology PhD student, I am hoping to utilize your tool for analyzing some single cell data in the lab.
Hi,
I attempted to run both the python notebook and bdtnp scripts and encountered some issues with both.
For
reconstruct_bdtnp_with_markers.py: My first commit downsamples cells to 3039 since that appears to be the number present in the current output image:3039_cells_3039_locations.png. I have replaced this image since it seems like the point sizes are better now. I also kept the updates toresults.txtandsdge_3039_cells_3039_locations, although I can drop these if you would prefer.Before:
After:
For
reconstruct_drosophila_embryo_tutorial.ipynb: My second commit contains numerous fixes to the python notebook, although my output still doesn't appear right. Any advice would be appreciated on producing the last 6 figures of various gene expression in the embryo. Fixes include:These changes allow me to run the entire notebook from start to finish without errors, but I still see some issues:
bdtnp.txt / dge.txt? It only contains 3039 cells, but the initial coords from geometry.txt includes 6078 cells.Before:
After:
Before:
After:
As a computational biology PhD student, I am hoping to utilize your tool for analyzing some single cell data in the lab.
Best, Patrick