blogtng:2010-06-17:imagej_-_imarisxt-imaris
Differences
This shows you the differences between two versions of the page.
Next revision | Previous revision | ||
blogtng:2010-06-17:imagej_-_imarisxt-imaris [2010/06/17 12:37] – created kota | blogtng:2010-06-17:imagej_-_imarisxt-imaris [2016/05/24 12:46] (current) – external edit 127.0.0.1 | ||
---|---|---|---|
Line 8: | Line 8: | ||
To use ImageJ along with Imaris, install ImageJ plugin from Bitplane as they instruct in Bitplane website. Then start up IJ. A small window that looks like below appears: | To use ImageJ along with Imaris, install ImageJ plugin from Bitplane as they instruct in Bitplane website. Then start up IJ. A small window that looks like below appears: | ||
- | {{: | + | {{ : |
By clicking " | By clicking " | ||
- | In this way, viewing 3D dataset in ImageJ stack could be viewed more comfortably in Imaris 3D user interface. One obvious problem I encountered is when I tired to export 4D dataset from ImageJ to Imaris. I opened a 4D dataset with 8 slices (z) and 46 time points. Since ImageJ plugin interface above does have user input for time point, I input the time points number but this was some how not recognized and stack was exported as 368 slices z-stack. | + | In this way, viewing 3D dataset in ImageJ stack could be viewed more comfortably in Imaris 3D user interface. |
+ | |||
+ | One obvious problem I encountered is when I tired to export 4D dataset from ImageJ to Imaris. I opened a 4D dataset with 8 slices (z) and 46 time points. Since ImageJ plugin interface above does have user input for time point, I input the time points number but this was some how not recognized and stack was exported as 368 slices z-stack. | ||
+ | |||
+ | -> Checking through the source code [[http:// | ||
+ | < | ||
+ | public boolean ExportDataSetToImaris(int aSelectedChannel, | ||
+ | </ | ||
+ | So probably, it will be same for channels: channels should be separated stack. | ||
+ | |||
+ | " | ||
+ | |||
+ | Other comments: | ||
+ | |||
+ | Macro file is available only with .txt extension, but it should also include " | ||
+ | < | ||
+ | if (!vFileName.endsWith(" | ||
+ | // a typical ImageJ macro file ends with .txt! | ||
+ | IJ.showMessage(" | ||
+ | return; | ||
+ | } | ||
+ | </ | ||
+ | |||
+ | Macro executer is a method in Adaptor class: | ||
+ | < | ||
+ | /** | ||
+ | * Apply a selected macro to Imaris DataSet | ||
+ | * | ||
+ | * @param aMacroDirectory The folder where the macro is lying | ||
+ | * aMacroFileName The filename of the macro | ||
+ | * aCreateNewChannels true if new channels should be created out of each existing ones | ||
+ | | ||
+ | * | ||
+ | * @return true if success | ||
+ | */ | ||
+ | | ||
+ | </ | ||
+ | |||
+ | This method basically import dataset (image in the current window, could include also multiple channels and time points), creates ImagePlus, apply macro, then after processing in IJ, The processed image is exported back into Imaris. | ||
+ | |||
+ | -> plugin would be better with more functionalities to import information such as surface, array of detected spot information, | ||
+ | |||
+ | ------ | ||
+ | **Extending the code**\\ | ||
+ | * extend bpImaris_Adapter.java (in my case for sending 4D) | ||
+ | * jniwrap.jar, | ||
+ | * latter package is com.bitplane.imaris.imaris.* | ||
+ | * exporting method (Current image stack in ImageJ to Imaris) is below. Iterate this to export time series. | ||
+ | < | ||
+ | public boolean ExportDataSetToImaris(int aSelectedChannel, | ||
+ | ... | ||
+ | </ | ||
+ | * ... should check if aCreateNewImage means new image within imaris. | ||
- | " | ||
blogtng/2010-06-17/imagej_-_imarisxt-imaris.1276778260.txt.gz · Last modified: 2016/05/24 12:46 (external edit)