Skip to content

Alice spatial #6

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
wants to merge 2 commits into
base: master
Choose a base branch
from
+188 −33
Open

Alice spatial #6

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
c07f208
add low thresh
aliceeeeeeeeee Apr 27, 2023
ff800bf
tiny update
aliceeeeeeeeee Jun 19, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
111 changes: 81 additions & 30 deletions Notebooks/notebook.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -57,7 +57,7 @@
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 2,
"metadata": {
"scrolled": false
},
Expand All @@ -67,10 +67,54 @@
"output_type": "stream",
"text": [
"Path to the folder of the movie(s) (in tiff format only) : \n",
" C:\\Users\\gros\\Desktop\\DATA\\20230207_fgf\\test\n",
"You have 1 movie(s), which is (are) :\n",
" C:\\Users\\gros\\Desktop\\DATA\\20221103_livedetection\\new_registration_062023\n",
"You have 1 movie(s), which is (are) : \n",
" gastr_SR_long_L1_Sum\n",
"Correct ? (1 for yes, 0 for no) \n",
" 1\n",
"\n",
"The dimensions of gastr_SR_long_L1_Sum are (200, 36, 2, 512, 512) . \n",
"\n",
"What is the order of the dimensions (for example TZCYX or XYZT) ? T stands for Time, C for channels if your image has multiple channels, Z for depth (or number or plans) and XY is your field of view. \n",
" TZCXY\n",
"\n",
"So gastr_SR_long_L1_Sum has 2 channels, 200 timepoints, the depth in z is 36 pixels and the XY plane measures 512 x 512 pixels.\n",
"Correct ? (1 for yes, 0 for no) \n",
" 1\n",
"Name of channel n°1 : \n",
" sulfo\n",
"Name of channel n°2 : \n",
" h2b\n",
"\n",
"Among the channels['sulfo', 'h2b'], you need a reference channel to compute the registration. A good option is generally a marker that is expressed ubiquitously\n",
"\n",
"Name of the reference channel : \n",
" h2b\n",
"\n",
"To register properly, you need to specify the voxel size of your input image. This can be found in Fiji, Image>Show Info. \n",
"Voxel size of your original image (XYZ successively) :\n",
" \n",
"X :0.62\n",
"Y :0.62\n",
"Z :2\n",
"Initial voxel size = [0.62, 0.62, 2.0]\n",
" \n",
"You can choose to have another voxel size on the registered image , for example to have an isotropic output image (voxel size [1,1,1]), Or you can also choose to keep the same voxel size. \n",
"Do you want to change the voxel size of your movies ? (1 for yes, 0 for no) : \n",
" 1\n",
"\n",
"Voxel size of your image after transformation (XYZ): \n",
" \n",
"2\n"
"X :1\n",
"Y :1\n",
"Z :1\n",
"\n",
"Voxel size after transformation = [1.0, 1.0, 1.0]\n",
"\n",
"You can choose to apply different transformation types depending on your data : ['rigid2D', 'rigid3D', 'translation2D', 'translation3D']\n",
"\n",
"Which one do you want to use ? (please enter the name of the transformation only, no other character) \n",
" rigid3D\n"
]
}
],
Expand All @@ -87,7 +131,7 @@
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 3,
"metadata": {},
"outputs": [
{
Expand All @@ -98,58 +142,65 @@
"Starting experiment\n",
"The registration will run with the following arguments:\n",
"\n",
"---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- File format -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------\n",
"path_to_data : C:\\Users\\gros\\Desktop\\DATA\\20230207_fgf\\test/2_sulfo/stackseq/\n",
"--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- File format ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------\n",
"path_to_data : C:\\Users\\gros\\Desktop\\DATA\\20221103_livedetection\\new_registration_062023/gastr_SR_long_L1_Sum_h2b/stackseq/\n",
"file_name : movie_t{t:03d}.tif\n",
"trsf_folder : C:\\Users\\gros\\Desktop\\DATA\\20230207_fgf\\test/2_sulfo/trsf/\n",
"output_format : C:\\Users\\gros\\Desktop\\DATA\\20230207_fgf\\test/2_sulfo/output/\n",
"trsf_folder : C:\\Users\\gros\\Desktop\\DATA\\20221103_livedetection\\new_registration_062023/gastr_SR_long_L1_Sum_h2b/trsf/\n",
"output_format : C:\\Users\\gros\\Desktop\\DATA\\20221103_livedetection\\new_registration_062023/gastr_SR_long_L1_Sum_h2b/output/\n",
"check_TP : 0\n",
"\n",
"----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Time series properties -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------\n",
"voxel_size : 0.620000x0.620000x1.000000\n",
"---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Time series properties ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------\n",
"voxel_size : 0.620000x0.620000x2.000000\n",
"first : 0\n",
"last : 101\n",
"last : 199\n",
"\n",
"---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Registration ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------\n",
"--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Registration --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------\n",
"compute_trsf : 1\n",
"ref_TP : 51\n",
"trsf_type : translation2D\n",
"ref_TP : 100\n",
"trsf_type : rigid3D\n",
"padding : 1\n",
"lowess : 0\n",
"trsf_interpolation : 0\n",
"recompute : 1\n",
"apply_trsf : 1\n",
"projection_path : C:\\Users\\gros\\Desktop\\DATA\\20230207_fgf\\test/2_sulfo/proj_output/\\\n",
"projection_path : C:\\Users\\gros\\Desktop\\DATA\\20221103_livedetection\\new_registration_062023/gastr_SR_long_L1_Sum_h2b/proj_output/\\\n",
"image_interpolation : linear\n",
"\n",
"0h:0min:30s\n",
"{'XResolution': 0.62, 'YResolution': 0.62, 'spacing': 1.0}\n",
"{'XResolution': 1.0, 'YResolution': 1.0, 'spacing': 1.0}\n",
"{'XResolution': 1.0, 'YResolution': 1.0, 'spacing': 1.0}\n",
"{'XResolution': 1.0, 'YResolution': 1.0, 'spacing': 1.0}\n",
"0h:1min:1s\n",
"{'XResolution': 0.62, 'YResolution': 0.62, 'spacing': 2.0}\n",
"Failure of {'path_to_data': 'C:\\\\Users\\\\gros\\\\Desktop\\\\DATA\\\\20221103_livedetection\\\\new_registration_062023/gastr_SR_long_L1_Sum_h2b/stackseq/', 'file_name': 'movie_t{t:03d}.tif', 'trsf_folder': 'C:\\\\Users\\\\gros\\\\Desktop\\\\DATA\\\\20221103_livedetection\\\\new_registration_062023/gastr_SR_long_L1_Sum_h2b/trsf/', 'output_format': 'C:\\\\Users\\\\gros\\\\Desktop\\\\DATA\\\\20221103_livedetection\\\\new_registration_062023/gastr_SR_long_L1_Sum_h2b/output/', 'projection_path': 'C:\\\\Users\\\\gros\\\\Desktop\\\\DATA\\\\20221103_livedetection\\\\new_registration_062023/gastr_SR_long_L1_Sum_h2b/proj_output/', 'check_TP': 0, 'voxel_size': [0.62, 0.62, 2.0], 'voxel_size_out': [1.0, 1.0, 1.0], 'first': 0, 'last': 199, 'not_to_do': [], 'compute_trsf': 1, 'ref_TP': 100, 'trsf_type': 'rigid3D', 'padding': 1, 'recompute': 1, 'apply_trsf': 1, 'out_bdv': '', 'plot_trsf': 0}\n",
"The requested file do not exist: C:\\Users\\gros\\Desktop\\DATA\\20221103_livedetection\\new_registration_062023/gastr_SR_long_L1_Sum_h2b/output/movie_t159.tif\n",
"\n",
"Starting experiment\n",
"The registration will run with the following arguments:\n",
"\n",
"------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- File format --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------\n",
"path_to_data : C:\\Users\\gros\\Desktop\\DATA\\20230207_fgf\\test/2_h2B/stackseq/\n",
"------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ File format ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------\n",
"path_to_data : C:\\Users\\gros\\Desktop\\DATA\\20221103_livedetection\\new_registration_062023/gastr_SR_long_L1_Sum_sulfo/stackseq/\n",
"file_name : movie_t{t:03d}.tif\n",
"trsf_folder : C:\\Users\\gros\\Desktop\\DATA\\20230207_fgf\\test/2_sulfo/trsf/\n",
"output_format : C:\\Users\\gros\\Desktop\\DATA\\20230207_fgf\\test/2_h2B/output/\n",
"trsf_folder : C:\\Users\\gros\\Desktop\\DATA\\20221103_livedetection\\new_registration_062023/gastr_SR_long_L1_Sum_h2b/trsf/\n",
"output_format : C:\\Users\\gros\\Desktop\\DATA\\20221103_livedetection\\new_registration_062023/gastr_SR_long_L1_Sum_sulfo/output/\n",
"check_TP : 0\n",
"\n",
"-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Time series properties --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------\n",
"voxel_size : 0.620000x0.620000x1.000000\n",
"------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Time series properties ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------\n",
"voxel_size : 0.620000x0.620000x2.000000\n",
"first : 0\n",
"last : 101\n",
"last : 199\n",
"\n",
"------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Registration -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------\n",
"------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Registration -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------\n",
"compute_trsf : 0\n",
"apply_trsf : 1\n",
"projection_path : C:\\Users\\gros\\Desktop\\DATA\\20230207_fgf\\test/2_h2B/proj_output/\\\n",
"projection_path : C:\\Users\\gros\\Desktop\\DATA\\20221103_livedetection\\new_registration_062023/gastr_SR_long_L1_Sum_sulfo/proj_output/\\\n",
"image_interpolation : linear\n",
"\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Failure of {'path_to_data': 'C:\\\\Users\\\\gros\\\\Desktop\\\\DATA\\\\20221103_livedetection\\\\new_registration_062023/gastr_SR_long_L1_Sum_sulfo/stackseq/', 'file_name': 'movie_t{t:03d}.tif', 'trsf_folder': 'C:\\\\Users\\\\gros\\\\Desktop\\\\DATA\\\\20221103_livedetection\\\\new_registration_062023/gastr_SR_long_L1_Sum_h2b/trsf/', 'output_format': 'C:\\\\Users\\\\gros\\\\Desktop\\\\DATA\\\\20221103_livedetection\\\\new_registration_062023/gastr_SR_long_L1_Sum_sulfo/output/', 'projection_path': 'C:\\\\Users\\\\gros\\\\Desktop\\\\DATA\\\\20221103_livedetection\\\\new_registration_062023/gastr_SR_long_L1_Sum_sulfo/proj_output/', 'check_TP': 0, 'voxel_size': [0.62, 0.62, 2.0], 'voxel_size_out': [1.0, 1.0, 1.0], 'first': 0, 'last': 199, 'not_to_do': [], 'compute_trsf': 0, 'ref_TP': 100, 'trsf_type': 'rigid3D', 'padding': 1, 'recompute': 1, 'apply_trsf': 1, 'out_bdv': '', 'plot_trsf': 0}\n",
"The requested file do not exist: C:\\Users\\gros\\Desktop\\DATA\\20221103_livedetection\\new_registration_062023/gastr_SR_long_L1_Sum_sulfo/output/movie_t013.tif\n"
]
}
],
"source": [
Expand Down
Binary file added User-manual/installation/installation_manual.pdf
View file
Open in desktop
Binary file not shown.
Loading