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The end goal is to build a web application where people can explore the historical maps I've georeferenced - among other things. ArcGIS online is the ideal venue for everything else I want, but for whatever reason it seems I can't easily upload raster files as in ArcMap. And I have approx. 12 rasters I want to upload (about the size of Bermuda).

There seems to be some confusing work arounds, but my concern is that a lot of credits will be used. Also, even more importantly, it seems I have to publish my rasters as layer files to ArcGIS online as a work around, but I feel this makes my work public to use by other users. I want only those in my organization to be able to access and use my georeferenced work in their maps. The work I've performed isn't mine to share, it belongs to my educational institution.

What's the best route for me to go? Is there a way to publish these layers to ArcGIS Online in a way that makes the layers accessible only to my organization?

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To reduce credit usage first build tile packages in ArcMap or Pro. Then you will upload the tpks to AGOL which will create a hosted tile service of your raster data. Then you can have control to share the layer to your organization and not to everyone. This will keep the content inside your organization and will not be accessible to users outside your org.

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From your original post it sounds like you may have already found info on how to publish tile layers online, but here's a link to the step-by-step process I used when I've done this in the past (I followed the "Define and publish a map in ArcMap" instructions): http://doc.arcgis.com/en/arcgis-online/share-maps/publish-tiles.htm

If your ESRI license is through your educational institution, make sure that your administrator gives your account the privileges to publish tile layers; I had to ask for it.

Also, you can still limit access to these layers like other maps/KMLs. On the My Content page, select the tile layer you just uploaded and click "Share" at the top of the window. Then check who you want to have access to your files (you can even limit access to a specific group smaller than your organization; see below).

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