Describe the bug
The algorithm allows for selection of specific wells to analyze, instead of the entire dataset (i.e., by using the wells option in the config YAML):
This feature is mainly used in development to speed up testing times; I'm not aware of it being used at all in production settings.
There are two issues with this feature:
The steps to run Cellpose includes renaming all the images (sidenote: this won't be necessary if Cellpose is updated in the Docker image, as the IO bug was fixed as of v2.1.1, see here for details) in the input folder using a glob pattern and then running the command on the entire direction:
This is a hacky workaround for using Cellpose, and it's fine when the analysis is running remotely and deletion of input files isn't a problem. When run locally, where the input folder might include the only copy of the raw image data, this is serious problem and could result in data loss.
There is a bug that will throw an image not found error if only a single well is selected. This is caused by this line:
The zip() function makes two sets iterable; this approach works fine if both wells and plate_paths are lists of the same length. If they are strings (which is the case when only one well is selected), it splits the string into individual characters - ['A', '0', '1'] for well, for example.
A quick solution to this would be to make sure wells and plate_paths are lists, and convert them if not.
Describe the bug The algorithm allows for selection of specific wells to analyze, instead of the entire dataset (i.e., by using the
wellsoption in the config YAML):https://github.com/zamanianlab/wrmXpress/blob/810989c45ce7fe0f2b2722b2634a39af98a7626f/local_env/parameters_template.yml#L92-L94
This feature is mainly used in development to speed up testing times; I'm not aware of it being used at all in production settings.
There are two issues with this feature:
The steps to run Cellpose includes renaming all the images (sidenote: this won't be necessary if Cellpose is updated in the Docker image, as the IO bug was fixed as of v2.1.1, see here for details) in the input folder using a glob pattern and then running the command on the entire direction:
https://github.com/zamanianlab/wrmXpress/blob/810989c45ce7fe0f2b2722b2634a39af98a7626f/wrapper.py#L91-L103
In order to not run Cellpose on images that the user doesn't want analyzed, the non-selected input images are deleted:
https://github.com/zamanianlab/wrmXpress/blob/810989c45ce7fe0f2b2722b2634a39af98a7626f/wrapper.py#L63-L76
This is a hacky workaround for using Cellpose, and it's fine when the analysis is running remotely and deletion of input files isn't a problem. When run locally, where the input folder might include the only copy of the raw image data, this is serious problem and could result in data loss.
There is a bug that will throw an image not found error if only a single well is selected. This is caused by this line:
https://github.com/zamanianlab/wrmXpress/blob/810989c45ce7fe0f2b2722b2634a39af98a7626f/wrapper.py#L139
The
zip()function makes two sets iterable; this approach works fine if bothwellsandplate_pathsare lists of the same length. If they are strings (which is the case when only one well is selected), it splits the string into individual characters -['A', '0', '1']forwell, for example.A quick solution to this would be to make sure
wellsandplate_pathsare lists, and convert them if not.The error gets thrown whenever the first image is loaded by the chosen modules, for example here when analyzing images of microfilariae:
https://github.com/zamanianlab/wrmXpress/blob/810989c45ce7fe0f2b2722b2634a39af98a7626f/modules/segment_worms.py#L118
To Reproduce Run wrmXpress locally using the attached YAML and sample data.
20210819-p01-NJW_753.txt 20210819-p01-NJW_753.zip