Hello everyone,
I’m a student working on wing data, but I’m very new to the world of ImageJ/micaToolbox and macro coding. I’ve been using the “Generate Multispectral Image” function to create .mspec files. However, I’ve run into a few predicaments.
- I have several hundred images that I need to get through, and from what I’ve seen online so far there is no means of batch processing my RAW image files to produce .mspec files. Is there a method to do so?
- If it is not possible to batch process, would it be possible to somehow set an ROI over the grey standard during the “Select _% standard” pop-up, for each time I open a new image. I ask since, all the RAW images have the grey standard in the exact same position. I’ve tried creating an ROI shortcut, but it does not appear to work.
- Finally, I was also wondering if there was some way to edit the code (or utilize any existing functions) to ensure the .mspec file is named the same as the RAW image used to create it. I have to keep copy-pasting the name of the image into the “Image Name” dialogue box every single time. Normally this works, however this time I have quite a lot of images.
Apologies if these questions are quite silly or if I am asking for too much. If there are any solutions to these problems, a breakdown would be greatly appreciated.
Thank you! =)
Heya,
Creating mspecs is still manual and labour intensive, for the better, or the worse. I know of people who have modified the process by implementing some basic computer vision tools to detect the standard and process things automatically or semi-automatically. Sadly, these tools have not been shared with me or the wider community. Maybe the ‘create MSPEC from Screening’ tool can help here? I would not be too familiar with how to go about combining the screening function with creating mspecs, but this might be an existing solution to your problem.
For now, if the grey standards are always the same, I could recommend hard-coding the precise values that the ‘Generate Multispectral Image’ script is using downstream and then write a macro that opens all the images in a folder. You would have to tinker with the output file naming so that it uses the original file name. This should also be possible to modify in the ‘Generate Multispectral Image’ script.
Cheers,
Cedric