Deconwolf GUI v0.0.7

This repo contains an optional GUI for deconwolf, or rather a command line builder.

Usage

Here is the intended workflow:

1. Drag and drop some tif files on the wolf in the first tab.

2. Head over to the Files tab to check that the channel names were identified automatically. By default the program expects that files follow the convention channel_###.tif for example dapi_001.tif would be identified as an image stained by dapi. If you use some other convention, you can configure that by setting a custom regular expression for channel identification under Config in the menu bar.

3. Go the the tab Channels and configure each channel, i.e. set the number of iterations per channel and specify the emission maxima. Hit the save button in the bottom.

4. Got to the Microscope tab and select microscope that was used, or create a new configuration using the basic optical parameters that is asked for. Don't forget to save.

5. Go to the Deconwolf tab to see if you want to use some other settings than the
   default ones.

6. Go to Run tab. Inspect the commands that will run and finally copy and paste into a terminal (use powershell on windows). The script can also be saved to disk with the "save" button. Save as a .ps1 file under windows or as a .sh file under Linux/mac.

Build and Install

There are pre-compiled binaries for Ubuntu and Windows under releases. If your platform is missing, please create a new issue.

If you prefer to build by yourself or use some other platform, see INSTALL.md.

Notes

• Most likely there are bugs and they can only be fixed when they are known. Please open a new ticket if you have any issues with the program.

• Some changes are planned for the future, see the TODO.md and also open issues.

• This gui plays well with nd2tool which converts .nd2 files (Nikon) to tif files. nd2tool is also capable of generating shell scripts for deconvolution with deconwolf.