Frequently Asked Questions
How to install OpenSegSPIM?
download the setup file . double click and follow instructed steps. OpenSegSPIM requires to first install the Matlab runtime library (included in the setup file). Error may appear if the computer already have a matlab runtime library that doesn't correspond to the Matlab version (R2011a) used to deploy the binary file. Make sure you have the Right version of the MCR.
Why is the image enhancement step too slow?
1. May be due to a too large nuclei. typically with a 10x to 40x (Typical for LSFM) nuclei should be in the 10 to 30 pix range. If resolution is high and nuclei are larger, both the noise removal as well as the smoothing part may take longer time
How to edit seeds manually
U can edit seeds manually after a full process of the data, the add seeds and remove seeds toolbar will be made enable after the Analysis. click on an existing seed to remove it or click on an empty space to add a new seed. after editing all the seeds reprocess the segmentation and analysis part to see the new result
How to batch process my files
The files to be batch processed should be data that are similar (typically a time lapses) first process one of the stack (i.e a reference stack) separately in order to get the setting files. Once user have processed one stack , the batch process will use the settings file to automatically choose all parameter.The batch process cannot take into account any manual seeds editing done on the reference stack.
How to reload previously segmented images
The Validation push button allow you to reload a previously processed stack. Click on Validation and select the "segmentedfill.tif" or "Nucleisegmented2.tif" File. It will automatically load back the Results, allowing you to manually edit or reprocess the result.