Fish Embryo Screen - stoeter/Fiji-Tools-for-HCS GitHub Wiki
- This set of macros help to process and analyze images taken on the Opera that contain
- 3D information (Z-stacks)
- Information in neighboring images (stitching)
- Information in a special region of the image that cannot be segmented by other methods
- Helpful for large objects such as, whole organisms, 3D cultures, tissues…
- The method of screening fish embryos on the Opera is about to be published…
- Opera images (.flex)
- Z-stacks
- Fields in well without gaps, so that fields can be stiched
- Special order of field acquisition (details)
- After image acquisition one needs to run three macros sequentially.
-
Opera Stack Montage for Fish
- This macro converts .flex into .tif, stiches fields, does Z-projection
-
Select ROI for Segmentation
- This macro allows to draw ROI for segmentation by the user
-
Segment2D in ROI
- This macro segments image within ROI and measures object properties
- Input (what you need to have and do)
- .flex
- Manual drawing of ROI per well
- Adjusting segmentation parameter
- Output (what you will get)
- .tif, raw image stacks stitched to montage per channel
- .tif, Z-projected images stitched to montage per channel
- .png RBG merge of channels
- .zip for ROI and for object lists / outlines from and for Fiji
- .txt result tables for manual and / or segmentation analysis
- .png of segmentation channel with drawn ROI and segmentation outlines
- Choose fields next to each other that can be tiled later and save .sly on Opera
- Opera starts in the middle and chooses positions from top to bottom, but fields must be in a special order for montage later
- Special order is needed: from top left to bottom right within the well
- Manipulate the sublayout.sly file (is xml format) to obtain the right order of ‘points’ (see example XML and more details)