Presentation on theme: "Morphometric or 3D reconstruction Chinmaya Sadangi."— Presentation transcript:
Morphometric or 3D reconstruction Chinmaya Sadangi
Outline Define Morphometric Image J Simple Neurite tracer plugin Guide to reconstruction using image J
Morphometry Studies on brain shape has given immense data Morphometric measurements have been obtained from brain regions that can be clearly defined and results in a lot of findings related to these measurements. Used for localizing significant structural differences, or overall brain structure. Also used for characterizing essential differences or for classification.
3D Reconstruction To understand the neuronal morphology To investigate neuronal function Understand the complicated relation between physiology (function) & morphology (form) of neurons. Characterization of cell types & investigation of neuronal development.
Open imageJ 64 bits If image is in.oib format convert it to.tiff format as shown in the dig.
Simple Neurite tracer Semi-automatic tracing of neurons. Efficiently find the best path between points in neurons. Measurement of neuron length & volume, 3D visualization. Best suited for fast tracing of higher order neural branches. Bioinformatics (2011):Mark H. Longair. Simple neurite tracer: open source software for reconstruction, visualization, & analysis of neuronal processes.
Go to plugins – segmentation – simple neurite tracer
New dialog box – convert image to 8 bits. This dialog box won’t appear if image is already in 8-bits Another dialog box – No 3D view
2 new window opens You can chose different color
Use Parts in nearby slices If you have a saved trace file you can load it using FILE – LOAD TRACES/SWC FILE
You can select a different background. Go to LUT – dropdown menu ---- select your choice. For eg: selecting FIRE (LUT) would give something like this.
Click on the cell body --- first start point Click at an end point to complete a path
Click on YES to confirm path. Alternatively, PRESS “Y” To complete path click on complete path. Alternatively, PRESS “F”
Traced path shows up in “All path” window You can designate it as soma, axon, dendrite
To save the trace file --- Go to FILE --- SAVE TRACE FILE
All path should be connected to the soma. If there is something not connected, check for the floating branch. How to know if you are doing it correctly?
How to identify an axon and a dendrite? An axon would be thinner as compared to a dendrite An axon branches extensively. An axon usually branches from a dendrite or the soma
Place both images side by side Select areas in both of them Crop them using control+shift+x Convert both of them to 8 bits
Go to plugins --- stiching --- Depreciated--- 3D stiching
A new dialog box would appear. Check first stack and second stack Go to fused image --- select max intensity Once the stiching starts,a log appears and shows STARTING and when it ends it appears FUSION COMPLETED
Keyboard shortcuts Y --- confirms current path F – Finishes current path N – cancels temporary path G – Select nearby path + -- Zooms in - (--) Zooms out
Why use TIFF images? (TAGGED IMAGE FILE FORMAT TIFF images format are LOSSLESS. Lossless – file is uncompressed & of higher image quality. JPEGS & other file format are LOSSY. Compressing image takes away quality of image. Image turned to JPEG can’t be reverted back