Hi, I'd like to inquire if it's possible to provide the dapi images inside your example, including osmFISH and MERFISH data, or can you tell us how to get it. Thank you!

Hi,

To run on the data, https://github.com/kharchenkolab/BaysorAnalysis/tree/master/data, do you have instructions on how to run baysor on these samples? I am unable to reproduce the figures from https://github.com/kharchenkolab/BaysorAnalysis/blob/master/notebooks/segmentation_free/segmentation_free_allen_smfish.ipynb

Thanks!

Hi team!
Fantastic work! I was able to run baysor on my data and get the expected output. I just have one simple question.
When you select the area to plot, how you decide the coordinates to select?

subset_coords = [
    ((-2872, -2822), (-2371, -2300)), 
    ((-2820, -2770), (-2300, -2325)),
    ((-2715, -2665), (-2350, -2275)),
    ((-2400, -2300), (-2750, -2600)),
    ((-2410, -2310), (-3225, -3075))
];

plt = B.plot_dataset_colors(@where(df_spatial, :x .>= -3180, :x .<= 800, :y .<= 3410, :y .>= -2370), :color, polygons=polygons, min_molecules_per_cell=50,
    min_pixels_per_cell=7, polygon_alpha=0.5, ms=1.0, polygon_line_width=1.5, ticks=false)[1];

for ((xs, xe), (ys, ye)) in subset_coords
    plt = Plots.plot([xs, xs, xe, xe, xs], [ys, ye, ye, ys, ys], color="black", label="", lw=4.0, alpha=0.75)
end

@time Plots.savefig(plt, "$plot_dir/polygons.png");
display(plt)
Plots.closeall()

Sorry for this silly question because I have very limited coding skill on Julia.
Thanks for developing this tool
Zhang

Hello,

I've installed Baysor using Julia inside a Docker container, but I'm having trouble accessing it directly from the terminal. While Docker works, it's a bit complex, and I'd prefer to use Julia directly. Even when navigating to the directory where Julia is stored, I can't seem to open Baysor. Could you guide me on how to set the correct path or any other solution?

Thanks for your assistance.