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HomeHomeGetting Started...Getting Started...How to…How to…How to save statistics from multiple datasets into one file?How to save statistics from multiple datasets into one file?
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How to save statistics from multiple datasets into one file?
 

With Imaris 8.0 it is indeed possible to generate statistic exports for multiple datasets into one Excel file. This is a feature of the new Arena data management tool.
1) Add a Collection to Arena
2) To manually fill this Collection drag&drop objects from the 'Objects tab' of the dataset onto the Collection. The Objects Tab you can see as soon as a dataset is selected and includes any objects.
3) 'RIGHT-MOUSE - Export Statistics' to generate e.g. an Exel file which holds the statistics of all that datasets.
Batch will create the Collection automatically but like above you can do so as well manually.

 
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Hi Dieter,

We have 100 datasets and each dataset contains 3-5 reconstructed cells where we measured the soma size (Spots wizard) and the neuronal projections (Filament wizard). Can we extract the statistics for Spots and Filaments in bulk according to each sub-object (named with unique ID) within each dataset? And can we apply the method described your original post to the 100 datasets containing the sub-objects?

Otherwise what would be the quickest workaround to avoid having to do every export manually? I was thinking of saving Spots objects in one .ims file and Filament objects in another.

Thanks,
Tuan
 
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Dieter Göhlmann wrote:

With Imaris 8.0 it is indeed possible to generate statistic exports for multiple datasets into one Excel file. This is a feature of the new Arena data management tool.
1) Add a Collection to Arena
2) To manually fill this Collection drag&drop objects from the 'Objects tab' of the dataset onto the Collection. The Objects Tab you can see as soon as a dataset is selected and includes any objects.
3) 'RIGHT-MOUSE - Export Statistics' to generate e.g. an Exel file which holds the statistics of all that datasets.
Batch will create the Collection automatically but like above you can do so as well manually.

Thu, 21 May 2015 08:48:08 GMT

 Hi,


I'm using Imaris 9.0.1, and I'm having some trouble with doing this. I have created a collection with the objects I'm interested in getting data from. When I "Export Statistics" however, I only get individual values for each part of the object (like each spot from a spots object, or every single spine separately from a Filaments object). These individual objects have no ID, and I can see no way to get average values, instead of individual ones. Further, only some of the statistics that I've selected in the Preferences->Statistics section get exported, while other values don't get exported. How can this be solved?


 
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Tuan Leng Tay wrote:
Hi Dieter,

We have 100 datasets and each dataset contains 3-5 reconstructed cells where we measured the soma size (Spots wizard) and the neuronal projections (Filament wizard). Can we extract the statistics for Spots and Filaments in bulk according to each sub-object (named with unique ID) within each dataset? And can we apply the method described your original post to the 100 datasets containing the sub-objects?

Otherwise what would be the quickest workaround to avoid having to do every export manually? I was thinking of saving Spots objects in one .ims file and Filament objects in another.

Thanks,
TuanTue, 27 Jun 2017 13:35:48 GMT

 Dear Tuan,

You can save both object types in the same .ims file. However, you cannot mix different object types in a collection. A collection can only contain one specific object type e.g. Spots, or Surfaces, or Cells, or Filaments. If you have 2 object types in your datasets, you need to create 2 separate collections for the Spots objects and the Filament objects. You drag&drop the Spots object from the file to the Spots collection and the Filament object to the Filament collection. In the exported Excel file from each collection, you will have columns of the different IDs, including their parent ID object and to which file they belong. 

I hope this helps.

Regards,

Daniel

 
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RAJASHEKAR IYER wrote:
Dieter Göhlmann wrote:

With Imaris 8.0 it is indeed possible to generate statistic exports for multiple datasets into one Excel file. This is a feature of the new Arena data management tool.
1) Add a Collection to Arena
2) To manually fill this Collection drag&drop objects from the 'Objects tab' of the dataset onto the Collection. The Objects Tab you can see as soon as a dataset is selected and includes any objects.
3) 'RIGHT-MOUSE - Export Statistics' to generate e.g. an Exel file which holds the statistics of all that datasets.
Batch will create the Collection automatically but like above you can do so as well manually.

Thu, 21 May 2015 08:48:08 GMT

 Hi,


I'm using Imaris 9.0.1, and I'm having some trouble with doing this. I have created a collection with the objects I'm interested in getting data from. When I "Export Statistics" however, I only get individual values for each part of the object (like each spot from a spots object, or every single spine separately from a Filaments object). These individual objects have no ID, and I can see no way to get average values, instead of individual ones. Further, only some of the statistics that I've selected in the Preferences->Statistics section get exported, while other values don't get exported. How can this be solved?


Thu, 18 Jan 2018 10:41:57 GMT

 Hi Rajashekar,

you only can export the statistics which are indeed checked in the preferences. If you need to export some which aren't checked, you need to check these and redo the export. The statistics are always re-calculated prior the export.

By default when exporting statistics from a collection in Arena, you should have in the various statistical tabs (except the Overall tab) columns of the object IDs, OriginalID, Original Component Name, Original Component ID, Original Image Name and Original Image ID (the latter one is not much of use as it's mainly for the internal Arena storage).

Average values aren't exported with this function. You can easily use the average function within Excel.

I hope this helps.

Regards,

Daniel

 
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