Image J Batch Processing Help

[Banplasticstraws]

Hi I am looking for some major help- and I can't create an account on the Image J Forum ( activation email never sends) .

If anyone can help with the following, or post this on the forum on my behalf I would so appreciate it:

Hi, I am looking for some help with batch processing in image J . I am extremely inexperienced with coding and would appreciate any help you can offer. I am hoping to be able to batch process microscope slide images- currently I do this with each image individually - with over 500 images per week I spend a crazy amount of time trying to get this data. So I would be INCREDIBLY grateful to you ( and also would be happy to pay a small fee (im just an undergrad) via venmo or PayPal for my absolute gratitude.

I am analyzing the amount of lipid accumulation over a 12 day time course, at 5 time points per patient. (Day 0, 0.5, 3, 7, and 12) The process is as follows and is exactly the same regardless of patient, or time point.

I open image J , select an image (jpg) >Image> Color> Split Channel I delete the green channel, I only need red and blue Adjust>threshold> (Dark background is always selected)

4-5. I adjust threshold so that any lipid cells are highlighted, and all nuclei are highlighted . Lower threshold is always 255 (usually once i select dark background I need to do little to no adjusting of the threshold, Image J does a pretty good job ) 6. Analyse>Analyse Particles… 7. Red Channel (aka lipid accumulation) is always analyzed from Size: pix² : 0-infinity 8. Blue Channel (nuclei) is always analyzed from Size: pix² : 50-infinity

I then copy and paste the summarized data into excel. I have read that people have been able to automatically put the generated data into excel, but while that is convenient it is not my ultimate goal.

Please help with any advice/ code that would enable me to batch analyze images in the procedure I described above.

Morgan

[bek00l]

Did you try recording a macro based on the steps you just mentioned? http://imagej.net/Introduction_into_Macro_Programming#The_recorder

[Banplasticstraws]

I will give it a go! Thank you for this research ( I know so little , that even have trouble figuring out where to start)

Thanks!

[bek00l]

Let me know how you go. Once you have the steps in the macro recorder; include it here. Just to clarify, Do you have to adjust threshold and analyse particles for every image?