<div dir="ltr"><div dir="ltr"><br></div><div dir="ltr">Dear Dr. Cuppit & Dr. Gutman,</div><div dir="ltr"><br></div><div dir="ltr">I am using the example MIRAX files from the OpenSlide Website,<div><br></div><div><a href="https://openslide.org/demo/">https://openslide.org/demo/</a> </div><div><br></div><div>Files:</div><div><br></div><div><a class="gmail-load-image" href="https://openslide.org/demo/#" title="Quick save of CMU-1.mrxs at 1/2 resolution (multiple images per position), brightfield, JPEG, CURRENT_SLIDE_VERSION 1.9" style="color:rgb(0,0,238);font-family:"Times New Roman";font-size:medium">CMU-1-Saved-1_2</a></div><div><a class="gmail-load-image" href="https://openslide.org/demo/#" title="Export of CMU-1.mrxs with overlaps resolved, brightfield, JPEG, CURRENT_SLIDE_VERSION 2.3" style="color:rgb(0,0,238);font-family:"Times New Roman";font-size:medium">CMU-1-Exported</a> <br></div><div><br></div><div>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.</div><div><b>Also, as mentioned earlier, I am trying to read "One Tile" out of the 4x4 tile structured blocks in level0. </b>I assumed the "DIGITIZER WIDTH" and "DIGITIZERHEIGHT" as the size of a single tile. Not sure if this assumption is correct or not.</div><div><br></div><div>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.</div><div><br></div><div>Sowri</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Sun, Jun 28, 2020 at 9:39 AM David Gutman <<a href="mailto:dagutman@gmail.com">dagutman@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="auto">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..</div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Sat, Jun 27, 2020, 8:38 PM Sowrirajan Sowmithran <<a href="mailto:ssowmith94@gmail.com" target="_blank">ssowmith94@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr">Sorry for the late reply.<div><br></div><div>Much thanks Dr. Cupitt for your suggestion.</div><div><br></div><div>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.</div><div>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 "<span style="color:rgb(0,0,0)">CameraImageDivisionsPerSide" = 4 means a 4x4 blocks but what is the actual size of this tile?</span><br></div><div><br></div><div><a href="https://lists.andrew.cmu.edu/pipermail/openslide-users/2012-July/000373.html" rel="noreferrer" target="_blank">https://lists.andrew.cmu.edu/pipermail/openslide-users/2012-July/000373.html</a> <br></div><div><br></div><div>Any help is much appreciated.</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Sat, Jun 13, 2020 at 5:40 AM <<a href="mailto:jcupitt@gmail.com" rel="noreferrer" target="_blank">jcupitt@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">On Fri, 12 Jun 2020 at 17:57, Sowrirajan Sowmithran<br>
<<a href="mailto:ssowmith94@gmail.com" rel="noreferrer" target="_blank">ssowmith94@gmail.com</a>> wrote:<br>
> 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?<br>
<br>
0 means transparent (ie. the slide background colour), so you are<br>
probably reading outside the image area. I would check the openslide<br>
bounds:<br>
<br>
"openslide.bounds-x",<br>
"openslide.bounds-y",<br>
"openslide.bounds-width",<br>
"openslide.bounds-height"<br>
<br>
And make sure you are inside them. You could also open the image file<br>
in a viewer and note the position of some real pixels.<br>
<br>
John<br>
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