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### Things addressed since 10/20/23:
- functions are now separate scripts and have well written docstrings/definitions
- README is expanded, now has examples for each function
### Need more work:…
lee-t updated
7 months ago
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I tried using starfish on a MERFISH image with Z = 4, C = 2 (4 depth planes and 2 fluorophore channels).
First I used the function write_experiment_json(), to seperate the image to 8 different image…
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Hi,
I was trying to work through the input data formatting and found that the links to the raw data to some of the sample datasets do not work. E.g.:
s3://czi.starfish.data.public/browse/raw/20180…
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Dear Brendan,
Sorry to bother you.
I wanted to generate the gene counts and metadata tables of individual cells profiled by MERFISH from the Moffit et al. 2018 raw data. And I followed the code …
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- [x] Introduction - scope 0.5-1 page
- look into reviews
- broad overview into the field
- mention nature methods "method of the year 2020"
- define axis: targeted/high-resolution vs unbiased…
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Hello,
I am trying to run the pyInfinityFlow pipeline and want to have all the observations.
It seems with the settings there is no clear option to have all the observations after running the pi…
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Thank you for this great tool and congratulations on the recent Nature publication!! I am wondering if you would recommend using CellOracle for spatially-resolved data, or would that violate any of th…
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Hi,
I am a fan of cell2location!
It was said that " Although the emerging SRT technologies, such as MERFISH, Slide-seq and Stereo-seq, had achieved cell-level or subcellular spatial resolution, so…
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Hi,
I'm encountering an issue with the SpatialFeatureExperiment (SFE) object when attempting to share data across different users. We have all our data stored on external data servers, which are moun…
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Hi,
I used cell2location to find the cell type annotation in the MERFISH data using correspoding scRNA-seq data. I used the N_cells_per_location=1, and detection_alpha=20 parameter for the traini…