Input a Micrograph

An MRC micrograph can be opened from Data: Micrograph: Load MRC. Upon completion, the system will be automatically switched to Micrograph OpPanel. Make sure the pixel resolution (Pixel Size) of the micrograph is set correctly. Signature also reads 2D SPIDER image (Data: Micrograph: Load SPD), which can then be save to an MRC file (Data: Micrograph: Save MRC) for further processing.

Sometimes it is necessary to pre-process a micrograph image before particle screening. A set of image processing functions are provided in 2D Image OpPanel for image intensity inversion, band-pass filtering, background removal, and more. When the pre-processing completes, the image can be saved to a new file from Data : Micrograph: Save MRC.

Image Quality Monitor

The intensity histogram (HSTG) of a properly scanned micrograph should assume a balanced bell-shape. To examine the spectrum of the image, click the SPEC button and set Box Size to a proper value. Position the mouse cursor to the region to be inspected, press CTRL and left-click. A box will be draw on the image, and the spectrum of the selected area will be displayed in the monitor. A usable micrograph image should not contain sever stigmation. If the spectrum deviates significantly from circular shape, mark the region with the Mark button (or CTRL+m). Systematically examine the entire micrograph. Upon completion, manually mask out the marked regions (see below). Note, however, that if too many regions are masked, the micrograph should be discarded.

Micrograph Masking

Masking can be performed both automatically and manually. In automatic masking, the local variance at each spot of the micrograph is compared to the overall variance. Regions with variances that are either too small or too large will be masked out. The thresholds are set by the two slidebars. VarBox sets the area for local variance evaluation. Margin sets the image edge exclusion. As for manual masking, available tools (accessed from Toolbar) include circle masking, line masking, free-hand drawing and erasing. Brush sets the size of drawing mark. The Clear button removes the existing mask except for the edge exclusion, which should be no less than the size of the particle of interest.

Keynote

A text note can be taken here for the micrograph being processed. Useful information may include imaging parameters and data processing history. This note will be displayed whenever the corresponding particle screening project is opened. The message should be brief and concise, since there is a 1024-character length limit.

Intensity Adjustment

The image intensity adjustment (brightness and contrast) is for display purpose only and has no effect on the computational screening. These knobs are multi-functional and are independent for image, template and particle display.