Repeat cropping with MotiQ_Cropper
This guide was written on March 04, 2023.
MotiQ Cropper logs the ROIs that you select and saves them along with the cropped image. If you find out later that you missed out a cellular branch during cropping, you may repeat the cropping and use the selections you previously used and reapply them with modifications to include the missing branch.
In this guide you will find out how!
- Launch FIJI or ImageJ
- Open the original image from which you aim to crop cells by drag and drop into the status bar of FIJI / ImageJ.
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Launch MotiQ_Cropper via the menu entry Plugins > MotiQ > MotiQ Cropper.
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Select the settings for MotiQ_Cropper that you selected before and start MotiQ_Cropper.
- Drag and drop the ROI-Set .zip file from the previous cropping into the status bar of your ImageJ/FIJI.
- In turn the loaded ROIs will appear in the ROI Manager window that pops up.
- Select the image plane in which you want to start cropping using the bar below the image that you aim to crop and select the corresponding ROI from the previous cropping in the ROI Manager (The number at the end of each ROI's name indicates the stack position it belonged to).
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Eventually modify the ROI if needed and confirm it to move to the next stack image.
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Continue the cropping as usual until you reach the last stack image to be processed (read 10. - 14. before you finish the cropping!). During the cropping process, whenever you aim to pull up again an ROI from the previous cropping, select it from the ROI Manager as in 7. - 8.
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While you re-cropped the cell, the ROI Manager has also logged the newly cropped ROIs. You can see now that the old ROIs and the new ROIs are logged (the old ROIs are the ROIs on the top of the list in the ROI Manager). When you finish the cropping, MotiQ Cropper will save all ROIs from the ROI Manager as the ROI log.
- To avoid that you also save the "old" ROIs into the newly generated log file, delete them as follows. Click on the first "old" ROI in the ROI Manager. Then while holding shift on the keyboard click on the last "old" ROI in the ROI Manager.
- Now delete the selected ROIs by clicking on the "Delete" button in the ROI Manager.
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You will now have to set the ROI for the last stack image. Note that you might see a ROI now that was from the "old" ROIs and does not match. For this last stack image you unfortunately cannot use any "old" ROI. But you may use one of the previously selected "new" ROIs by selecting it in the ROI Manager and then may modify it to fit to the last stack image.
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Confirm the last ROI.
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Now the re-cropping is done. MotiQ Cropper will have generated a new output file in the directory where the original image was stored (as usual).
