diff --git a/examples/run_imageviewer.py b/examples/run_imageviewer.py index f9cadd0da295d675b4065b117423cdb73432fceb..6afe25efd5edc364897106162a29f0f2863f757e 100644 --- a/examples/run_imageviewer.py +++ b/examples/run_imageviewer.py @@ -1,18 +1,26 @@ -from wela.imageviewer import LocalImageViewer, get_files +from wela.imageviewer import ImageViewer - -aliby_input = "/Users/pswain/wip/aliby_input/" aliby_output = "/Users/pswain/wip/aliby_output/" -omero_name = "test26643" -position = "001" +omero_name = "2104_2024_03_29_Aggregation_to_0pc_glc_sorb_00" +position = "ch11_Gcd6_001" + +# ADD details +server_info = { + "host": "", + "username": "", + "password": "", +} -# for zarr files -liv = LocalImageViewer( - *get_files( - aliby_input, - aliby_output, - omero_name, - position, - ) +h5file = f"{aliby_output}{omero_name}/{position}.h5" +iv = ImageViewer.remote(h5file, server_info, 2104) +tpt_end = 10 +# for information only +iv.print_traps_with_cells(tpt_end) +# use Napari to view cells +# python -m pip install "napari[all]" --upgrade +iv.view( + trap_ids=[4, 8, 13], + tpt_end=tpt_end, + channels_to_skip=["cy5"], + no_vertical_tiles=1, ) -liv.view(trap_id=1, tps=8) diff --git a/examples/run_local_imageviewer.py b/examples/run_local_imageviewer.py new file mode 100644 index 0000000000000000000000000000000000000000..89b84b1e1968ae78c306cb3f8bdebaf93a721a2d --- /dev/null +++ b/examples/run_local_imageviewer.py @@ -0,0 +1,24 @@ +from wela.imageviewer import ImageViewer, get_files + + +aliby_input = "/Users/pswain/wip/aliby_input/" +aliby_output = "/Users/pswain/wip/aliby_output/" +omero_name = "25681_2022_04_30_flavin_htb2_glucose_10mgpL_01_00" +position = "htb2mCherry_018" + +# for zarr files +iv = ImageViewer.local( + **get_files( + aliby_input, + aliby_output, + omero_name, + position, + ) +) +tpt_end = 14 +iv.print_traps_with_cells(tpt_end=tpt_end) +iv.view( + tpt_end=tpt_end, + trap_ids=[1, 2, 3, 6, 48, 49, 50, 51, 52, 53, 54, 55, 87, 88, 92, 93], + no_vertical_tiles=3, +)