MouseLand
Let user define a custom name for the output image.
Is your feature request related to a problem? Please describe.
Currently the name of the output image is only built by adding the suffix cp_masks to the name of the input image, i.e. name_input_image_cp_masks.tif. . That naming convention is fixed and cannot be customized.
Describe the solution you'd like Include a new flag as part of the output arguments that enables the user to define the name of the output image.
Describe alternatives you've considered For example a flag called --output_name.
Type in the CLI: --output_name "custom_sample_name"
In the output folder one should get the file:
cutom_sample_name.tif
Additional context Standardizing input and output names comes in handy when pipelining. Some pipelines that are already built have standardized names. Hence, adding an output name flag will allow using cellpose within already established pipelines, e.g. MCMICRO.
Hi @VictorDidier, how do you imaging implementing this for running Cellpose on a directory of images? Maybe this would only work when running on a single image?
Hi @mrariden, yes you are right, this should be only implemented when running the segmentation on a single image.