From medupall at andrew.cmu.edu  Mon Jun 10 10:45:17 2019
From: medupall at andrew.cmu.edu (Manaswitha Edupalli)
Date: Mon, 10 Jun 2019 10:45:17 -0400
Subject: Issues w/ Installing and Using OpenSlide
Message-ID: <CAOCFFVBbJyZw4nOjaFs-OMThUABn0rwvBazQ+mFwJGeXQdyemw@mail.gmail.com>

 I have had great difficulty installing and using Openslide. In order to
install:
1) pip install openslide-python
2) I downloaded the binaries for python from https://openslide.org
3) pip install openslides
4) I downloaded the binaries for openSlide, because python is just the
wrapper?

Over the course of this process, I have been encountering the same issue:

Traceback (most recent call last):

  File "tiling_filtering.py", line 2, in <module>

    import openslide

  File
"/Users/mae4004/Library/Python/2.7/lib/python/site-packages/openslide/__init__.py",
line 29, in <module>

    from openslide import lowlevel

  File
"/Users/mae4004/Library/Python/2.7/lib/python/site-packages/openslide/lowlevel.py",
line 55, in <module>

    "Is OpenSlide installed?")

ImportError: Couldn't locate OpenSlide dylib.  Is OpenSlide installed?

I did some research, and it says the issue is that OpenSlide is not my
dylib search path. I have no idea how to add it. Im using a Mac OS Mojave V
10.14.2. Any suggestions?

I have tried installing by creating a Conda environment as well and I have
met with the same error. Any help would be much appreciated.


Thanks!
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From ruppmatt at gmail.com  Fri Jun 14 19:13:24 2019
From: ruppmatt at gmail.com (Matthew Rupp)
Date: Fri, 14 Jun 2019 19:13:24 -0400
Subject: Downsampled Read Regions Appear Faded
Message-ID: <CAJu2h041uf=+kbst8h8vNi=RfFu0AYs-EVgK7gUOf+S90dRzAg@mail.gmail.com>

Greetings-

I'm new to this, so bare with me please.

I'm using Python-OpenSlide to work with Aperio SVS scans.

If I'm reading a non-level-0 region, I encounter a phenomenon where the
resulting values display as faded.  Playing around by removing the alpha
channels, it has something to do with them (e.g. the image goes mostly
black).

However, as I shift the location being sampled one pixel at a time in
level-0, the fading goes away, and I'm left with a bright, sharp image my
that target level.  As I continue to move across the level-0 grid, the
image begins to fade again.

What's going on?

Cheers,
Matt
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