Phriction Projects Wikis Bioimaging And Optics Platform Image Processing Cell Profiler History Version 1 vs 2
Version 1 vs 2
Version 1 vs 2
Content Changes
Content Changes
=Changing file paths from Database file =
It is currently the case that the paths to the analysed images using Cell Profiler are all absolute, which makes moving or sharing the data for use in Cell Profiler Analyst difficult.
We provide a Python 3.5 script that will modify the resulting SQLite database in the following way:
1. It will look for the `image_table` and `image_names` values from the `Experiment_Properties` table
2. It will modify the `Image_PathName_??` column of 'image_table' to reflect the new location of the images for each `??` which corresponds to the image_names
3. It will modify the path of `db_sqlite_file` in the `Experiment_Properties` table.
WARNING: Make a copy of your database before using the script, as it will be overwritten.
WARNING: All images are assumed to be in the same folder. If this is not your case, Cell Profiler Analyst will no longer find your images.
=Changing file paths from Database file =
It is currently the case that the paths to the analysed images using Cell Profiler are all absolute, which makes moving or sharing the data for use in Cell Profiler Analyst difficult.
We provide a Python 3.5 script that will modify the resulting SQLite database in the following way:
1. It will look for the `image_table` and `image_names` values from the `Experiment_Properties` table
2. It will modify the `Image_PathName_??` column of 'image_table' to reflect the new location of the images for each `??` which corresponds to the image_names
3. It will modify the path of `db_sqlite_file` in the `Experiment_Properties` table.
WARNING: Make a copy of your database before using the script, as it will be overwritten.
WARNING: All images are assumed to be in the same folder. If this is not your case, Cell Profiler Analyst will no longer find your images.
https://c4science.ch/diffusion/3881/browse/master/ChangeImagePaths.py
Repository at r3881
=Changing file paths from Database file =
It is currently the case that the paths to the analysed images using Cell Profiler are all absolute, which makes moving or sharing the data for use in Cell Profiler Analyst difficult.
We provide a Python 3.5 script that will modify the resulting SQLite database in the following way:
1. It will look for the `image_table` and `image_names` values from the `Experiment_Properties` table
2. It will modify the `Image_PathName_??` column of 'image_table' to reflect the new location of the images for each `??` which corresponds to the image_names
3. It will modify the path of `db_sqlite_file` in the `Experiment_Properties` table.
WARNING: Make a copy of your database before using the script, as it will be overwritten.
WARNING: All images are assumed to be in the same folder. If this is not your case, Cell Profiler Analyst will no longer find your images.
https://c4science.ch/diffusion/3881/browse/master/ChangeImagePaths.py
Repository at r3881
c4science · Help