Pathotrainer

Case collections are the way to organize your WSIs to be shown in training sessions. Once you've made a Case Collection all the slides within it can quickly be added to as many training sessions as you like.

Sometimes you may find yourself in a situation with a lot of 'loose' WSI files in a folder, and you want to quickly put each one in it's own Case subfolder.

Thankfully, we've written a quick script for Windows Command Prompt that will help you get your WSIs in an organised state.

If you're using a filetype with just one file per WSI e.g. .dcm, .ndpi:

Step 1: Open Command Prompt (type CMD into the windows search bar and open the app)

Step 2: Navigate in Command Prompt to the folder with the WSIs. This is done by typing “cd” and then pasting the path to the folder. Then press enter.

Step 3: Now that you're in the right folder, copy and paste: for %i in (*) do mkdir “%~ni” then hit enter. Running this command will make a subfolder for every file, with the same as the file.

Step 4: Copy and paste then enter: for %i in (*) do move “%i” “%~ni”

If you're using a folder-based filetype e.g. .mrxs that has a folder and a file with the same name

Step 1: Open Command Prompt (type CMD into the windows search bar and open the app)

Step 2: Navigate in Command Prompt to the folder with the WSIs. This is done by typing “cd” and then pasting the path to the folder. Then press enter.

Step 3: Now that you're in the right folder, copy and paste: for /d %i in (*) do mkdir “%i_temp” then hit enter. Running this command will make a new folder for every folder in the directory, with the same name as the folder + “_temp”.

Step 4: Copy and paste then enter:
for /d %i in (*) do (
if /i not “%i”==“%i_temp” (
move “%i” “%i_temp\”
)
)

This will copy all your existing folders into the newly created “_temp” folders.

Step 5: Copy and execute for %i in (*) do move “%i” “%~ni_temp”
This will move all the loose files into the directory with the same name plus “_temp”

Please note that:

1. You can adjust the three “_temp” in all three commands to whatever addition you'd like, however it must be exactly the same for all three commands.
2. This script only works when the folder and the file both have exactly the same name - if this is not the case you will need to devise a custom script as we cannot anticipate all naming conventions.
3. If you have multiple WSIs that have to go into the same case, you will need to devise a custom script as we cannot anticipate what your combination of WSIs per case is.