Question about readRegion on MIRAX files

[Sowrirajan Sowmithran]

Dear Dr. Cuppit & Dr. Gutman,

I am using the example MIRAX files from the OpenSlide Website,

https://openslide.org/demo/

Files:

CMU-1-Saved-1_2 <https://openslide.org/demo/#>
CMU-1-Exported <https://openslide.org/demo/#>

Looking from the Image format, the values I noticed before was uint32. I
cast these values to uint8 format to get the final image. While this worked
great for the svs, MIRAX seems to differ.
*Also, as mentioned earlier, I am trying to read "One Tile" out of the 4x4
tile structured blocks in level0. *I assumed the "DIGITIZER WIDTH" and
"DIGITIZERHEIGHT" as the size of a single tile. Not sure if this assumption
is correct or not.

In the meantime let me also approach the issue from the angle Dr. Gutman
pointed out, and try casting the output of the openslide_readRegion to an
8-bit/ 16-bit data.

Sowri

On Sun, Jun 28, 2020 at 9:39 AM David Gutman <dagutman at gmail.com> wrote:

> Is the image dark or any chance the contrast and or max/min or window
> settings are just set improperly?   With 12 or 16 bit images sometimes at
> least in other formats I've seen it where the image range is set from 0 to
> 2x16 but the image is only hundreds or thousands of units bright.. so
> basically everything looks black because the range is goofed..
>
> On Sat, Jun 27, 2020, 8:38 PM Sowrirajan Sowmithran <ssowmith94 at gmail.com>
> wrote:
>
>> Sorry for the late reply.
>>
>> Much thanks Dr. Cupitt for your suggestion.
>>
>> No matter what region I read for a MIRAX file I keep getting the dark
>> region only. On the other hand I have no difficulties with the svs file.
>> One additional question is how do I determine the tile-size and block
>> size of the MIRAX file. I knew from the post by Benjamin that "CameraImageDivisionsPerSide"
>> = 4 means a 4x4 blocks but what is the actual size of this tile?
>>
>>
>> https://lists.andrew.cmu.edu/pipermail/openslide-users/2012-July/000373.html
>>
>>
>> Any help is much appreciated.
>>
>> On Sat, Jun 13, 2020 at 5:40 AM <jcupitt at gmail.com> wrote:
>>
>>> On Fri, 12 Jun 2020 at 17:57, Sowrirajan Sowmithran
>>> <ssowmith94 at gmail.com> wrote:
>>> > On trying to apply the openslide_readRegion() function to get the
>>> desired part (random area) of the data, I end up getting a dark image
>>> instead (all 0s). Does this have something to do with the MIRAX format or
>>> the region being empty? If it is the later how do I determine which region
>>> has data and display it?
>>>
>>> 0 means transparent (ie. the slide background colour), so you are
>>> probably reading outside the image area. I would check the openslide
>>> bounds:
>>>
>>>                 "openslide.bounds-x",
>>>                 "openslide.bounds-y",
>>>                 "openslide.bounds-width",
>>>                 "openslide.bounds-height"
>>>
>>> And make sure you are inside them. You could also open the image file
>>> in a viewer and note the position of some real pixels.
>>>
>>> John
>>> _______________________________________________
>>> openslide-users mailing list
>>> openslide-users at lists.andrew.cmu.edu
>>> https://lists.andrew.cmu.edu/mailman/listinfo/openslide-users
>>>
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>>
>
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