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paulrichards321 / jpg2svs

Convert Olympus ini jpeg Virtual Microscopy Slide files into one big tiff file readable by Aperio ImageScope, the openslide library, or OMERO Virtual Microscopy.
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Can I build it on visual studio 2015? #2

Open edwardlo12 opened 6 years ago

edwardlo12 commented 6 years ago

I have tried to build up i t on visual studio 2015, and i have already built up it sycessfully. But the program tell me it need msys*.dll. Is it means I can only build it up on MSYS2?

paulrichards321 commented 6 years ago

Sorry for the wait! Actually I successfully built it on Visual Studio and ran it, but don't remember what version I used. I think it was 2015. With msys2 it's just simpler because you can just use pacman to get all the dependencies. Are you sure you are running the right executable in the right folder? I am going to try to reproduce this and will get back to you.

edwardlo12 commented 6 years ago

ok thanks

edwardlo12 commented 6 years ago

i had build it up by msys but the outputfile can't be read by openslide both in c and python. Is the file aperio svs format? How can i build up .ini files?

paulrichards321 commented 6 years ago

Hi! Sorry for the wait.

Are you sure these jpeg tiles that you are trying to convert into a svs/tiff file come from an Olympus scanner? This isn't just a regular flatbed scanner. If you did have them scanned, you should have the .ini files already generated from the Olympus software. "FinalScan.ini", "FinalCond.ini", "SlideScan.ini", "SlideCond.ini" should already be in the same directory as the Olympus jpegs. They specify the coordinates and layer of each of the jpeg file in the pyramid. If you don't have them that it is going to be very difficult to build them manually. If you don't have these files than but know the "simple" coordinates of where each jpeg should be, let me know and maybe I can work something into the software. Currently the Olympus/Bacus coordinates are built using a different equation that makes putting this together manually pretty tricky.

Note: I have also included and uploaded a Visual C++ Makefile (I used Visual Studio 2015) and updated the INSTALL.txt instructions on how to build it with the Visual C++ compiler. There originally was no Makefile for Visual Studio but I have fixed that now!

paulrichards321 commented 6 years ago

Hi Edward,

I have investigated the issue with the openslide library and made quite a few updates to this program to get it to work with the openslide library. However, as mentioned before, you will need the ini files from the Olympus dataset. Tested with a git clone of the openslide library on 11/2/2018. Do a get clone of my own code to grab the latest update: git clone https://github.com/paulrichards321/jpg2svs

and then recompile with either msys2, Visual Studio 2015, or on linux (instructions provided for all three platforms - see README.txt).