| Both sides previous revision
Previous revision
Next revision
|
Previous revision
Next revision
Both sides next revision
|
docs:mm_dispim_plugin_user_guide [2019/02/23 00:06]
Jon Daniels [Multiple Positions (XY)] |
docs:mm_dispim_plugin_user_guide [2019/07/03 00:03]
Jon Daniels [Acquisition Mode] |
| |
| Currently several modes are supported: | Currently several modes are supported: |
| * Synchronous piezo/slice scan: standard use, the piezo and sheet move together through the sample | * Synchronous piezo/slice scan: standard piezo use, the piezo and sheet move together through the sample |
| * No scan (fixed sheet): neither the piezo nor light sheet moves; useful for characterizing vibration in the system | * No scan (fixed sheet): none of the piezo nor light sheet nor the stage moves (only the light sheet generation using the sheet axis); useful for characterizing vibration in the system |
| * Stage scan: uses the XY stage to move the sample through a fixed light sheet; for two-sided acquisitions, one view is collected in the first pass, and the second view is collected as the stage moves “back” for a second pass; see the document on stage scanning for details and requirements | * Stage scan: uses the XY stage to move the sample through a fixed light sheet; for two-sided acquisitions, one view is collected in the first pass, and the second view is collected as the stage moves “back” for a second pass; see the document on stage scanning for details and requirements |
| * Stage scan interleaved: same as stage scan except that the stage moves half as fast and the two light paths alternate, meaning both views are collected in the same pass; use caution if you are using a galvo to switch the laser between the sides, this can overstress some galvos | * Stage scan interleaved: same as stage scan except that the stage moves half as fast and the two light paths alternate, meaning both views are collected in the same pass; use caution if you are using a galvo to switch the laser between the sides, this can overstress some galvos |
| * Stage scan unidirectional: same as stage scan except the second view is taken while scanning in the same direction as the first view | * Stage scan unidirectional: same as stage scan except the second view is taken while scanning in the same direction as the first view with a rewind step between. For 1-sided acquisitions stage scan and stage scan unidirectional are equivalent. For 2-sided acquisitions the stage scan unidirectional will take slightly longer (the rewind step is done at 75% of the max stage speed) but makes data processing easier. |
| * Slice scan only: suppresses movement of piezo but moves the light sheet; useful for characterizing light sheet thickness | * Slice scan only: suppresses movement of piezo but moves the light sheet; useful for characterizing light sheet thickness and for autofocus |
| * Piezo scan only: the light sheet stays stationary but the piezo moves; useful for establishing axial PSF | * Piezo scan only: the light sheet stays stationary but the piezo moves; useful for establishing axial PSF and for autofocus |
| |
| |
| If the box is checked, the plugin will use Micro-Manager’s position list to acquire volumes and multiple locations. For each time point, every position is visited once. See Micro-Manager User’s Guide for more details on the [[https://micro-manager.org/wiki/Micro-Manager_User%27s_Guide#Position_List_Dialog|Position List Dialog]]. | If the box is checked, the plugin will use Micro-Manager’s position list to acquire volumes and multiple locations. For each time point, every position is visited once. See Micro-Manager User’s Guide for more details on the [[https://micro-manager.org/wiki/Micro-Manager_User%27s_Guide#Position_List_Dialog|Position List Dialog]]. |
| |
| For large samples there is a YZ grid creator (as of March 2018) so multiple strips can be collected covering a sample. The same GUI allows you to create a “grid” in X where, instead of specifying slice spacing, you specify start and stop positions, and spacing between them in stage coordinates. | For large samples there is a YZ grid creator (as of March 2018) so multiple strips can be collected covering a sample. Open the grid creator window by clicking on the "XYZ grid..." button. Select the axes that you want to create the grid in and click the "Compute grid" button to set up the grid. You can mark specific start/stop positions in live mode. The delta for Y and Z can be entered manually, or if you click the button "Set" next to those fields then the value is populated based on the camera ROI and the overlap percentage setting. Note that the X axis is used for stage scanning, so when you create a "grid" in X you are specifying start and stop positions and spacing between them in stage coordinates. |
| | |
| |
| === Overview Acquisition === | === Overview Acquisition === |
| |
| As of February 2019 there is a feature to acquire an overview acquisition. This is useful when the entire sample is many times larger than the instantaneous field of view. The overview image is a 2D image representing a thin slice of the sample which can be collected relatively quickly. After acquisition, a rectangle is placed on the overview image representing the current stage position, and this rectangle moves with the stage as long as positions are being updated. It is not intended for use with a Z grid but only Y grid. | As of March 2019 there is a feature to acquire an overview acquisition. This is useful when the entire sample is many times larger than the instantaneous field of view. The overview image is a 2D image representing a thin slice of the sample which can be collected relatively quickly. After acquisition, a rectangle is placed on the overview image representing the current stage position, and this rectangle moves with the stage as long as positions are being updated. It is not intended for use with a Z grid but only XY grid. |
| |
| Settings for the overview acquisition reside on the "Data Analysis" tab. These include the downsample factor for XY and for slice spacing. The fractional thickness specifies how much of the entire image will be max projected to form the overview image. You specify a channel and a side to run the overview acquisition with. | Settings for the overview acquisition reside on the "Data Analysis" tab. These include the downsample factor for XY and for slice spacing. The fractional thickness specifies how much of the entire image will be max projected to form the overview image. You specify a channel and a side to run the overview acquisition with. |
| |
| Perform the overview acquisition using the button in the "XYZ grid" window accessed from the acquisition tab. It uses the current position list. | Perform the overview acquisition using the button in the "XYZ grid..." window accessed from the acquisition tab. Running the acquisition uses the current settings of the grid GUI for X and Y (if they are enabled) and will overwrite any existing position list. |
| |
| |
