Detecting Nuclei

Open Image

  • Select card Open File

  • Browse for Image on your local workstation

  • Open the selected file

_images/open_file.png
CTRL+SHIFT allows you to Zoom In and Out
Mouse Scroll Wheel allows you to scroll through volumetric image

Local Minima in the 4D space

  • Select card Detect Spherical Structures

  • Set Min Scale = 5

  • Set Step Scale = 1

  • Set Max Scale = 9

  • Set Anisotropic Axis = X for in-situ embryo and Z for live embryo

  • Set Anisotropic Sampling Factor = 1 for in-situ embryo and 5 for live embryo

  • Ensure Bright Blobs checkbox is ticked

  • Press Run

Warning This step above takes the most time and memory.
If the above process fails, increase the memory allocated to Fiji by going to Edit>Options>Memory & Threads and increasing the Maximum Memory
Trouble Shoot If the above doesn’t work, try cropping out the background from the volumetric image just to process the embryo of interest
_images/detect_nuclei.png

Edit Nuclei

  • Select card Edit Detections

  • Press Run

  • Visually inspect the results

  • At sites of over-detection, select card Select Nuclei

  • Click on over-segmented detection and press Delete

  • At sites of under-detection, select card Select Nuclei

  • Drag, form an Oval and release. Next click Add

  • When satisfied, press Save Results

_images/add_nucleus.png _images/added_nucleus.png

Load Previous Detections

  • Open Image by using the card Open File

  • Select card Load Ground Truth Detections

  • Browse for previously saved csv results file

  • Click Open to load results file