Mitochondria to cell volume fractionator - mask debris
Parameters:
| Name |
# |
Type |
Description |
| Where to mask (inside or outside of ROI) |
1 |
string |
Whether fill area inside or outside of the area marked by the ROI |
Description:
Use this pipeline to mask debris during analysis of mitochondria:cell volume fraction. Draw ROIs to mask debris “Inside” or “Outside” of the ROI in the “Cell” or “Mitochondria” images obtained using any of the Mito:Cell Volume Fractionator pipelines. Masking will be applied only to the current frame. After removing debris or dead cells by ROI masking from use this pipeline “Mitochondria to cell volume fractionator - recalculate volume fraction” to get the volume fraction. See interactive volume fractionator protocol in the Primer.
• If dead cells (rounded up or lobed cells with no mitochondrial staining), debris or out-of-focus cells (diffuse edges of the cytosolic stain) are visible in the images remove them as follows:
o Press the synchronize button on the main toolbar to synchronize frame-to-frame scrolling of the windows.
o Identify and eliminate frames that contain no positively stained cells using the cut tool on the main toolbar, and pressing Cut current.
o On each frame, if necessary, draw an ROI around unwanted details, and run this pipeline.
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