Reading mrxs files

[Kedar Grama]

Hi,

I was going through the code in the test example and trying it on a few
.mrxs files that I have and writing out .ppm files of different layers.

The function call:
openslide_read_region(osr, buf, 0, 0, layer, w, h);

Only works on brightfield images but if I use it on multi-channel
florescence data it gives me only one channel. How do I access the other
channels or 'levels' in the image?

I see this in the properties printed out.
             property: mirax.LAYER_1_LEVEL_0_SECTION.ACTIVE -> ON
             property: mirax.LAYER_1_LEVEL_0_SECTION.BRIGHTNESS -> 0
             property: mirax.LAYER_1_LEVEL_0_SECTION.COLOR_B -> 255
             property: mirax.LAYER_1_LEVEL_0_SECTION.COLOR_G -> 0
             property: mirax.LAYER_1_LEVEL_0_SECTION.COLOR_R -> 0
             property: mirax.LAYER_1_LEVEL_0_SECTION.CONTRAST -> 0
             property:
mirax.LAYER_1_LEVEL_0_SECTION.DATA_IN_THIS_FILTER_LEVEL -> FilterLevel_0
             property: mirax.LAYER_1_LEVEL_0_SECTION.DIGITALGAIN -> 0
             property: mirax.LAYER_1_LEVEL_0_SECTION.EXPOSUREPERCENTAGE ->
100
             property: mirax.LAYER_1_LEVEL_0_SECTION.EXPOSURE_TIME -> 250000
             property: mirax.LAYER_1_LEVEL_0_SECTION.EXTENDED_STEP_COUNT ->
3
             property: mirax.LAYER_1_LEVEL_0_SECTION.EXTENDED_STEP_SIZE -> 1
             property: mirax.LAYER_1_LEVEL_0_SECTION.FILTER_NAME -> DAPI
             property: mirax.LAYER_1_LEVEL_0_SECTION.FILTER_REAL_POSITION ->
0
             property: mirax.LAYER_1_LEVEL_0_SECTION.GAMMA -> 1
             property: mirax.LAYER_1_LEVEL_0_SECTION.IS_MASTER_FILTER ->
True
             property: mirax.LAYER_1_LEVEL_0_SECTION.IS_STITCHING_FILTER ->
1
             property: mirax.LAYER_1_LEVEL_0_SECTION.MODIFIED_COLOR_B -> 255
             property: mirax.LAYER_1_LEVEL_0_SECTION.MODIFIED_COLOR_G -> 0
             property: mirax.LAYER_1_LEVEL_0_SECTION.MODIFIED_COLOR_R -> 0
             property: mirax.LAYER_1_LEVEL_0_SECTION.MODIFY -> ON
             property: mirax.LAYER_1_LEVEL_0_SECTION.STORING_CHANNEL_NUMBER
-> 0
             property: mirax.LAYER_1_LEVEL_0_SECTION.THRESHOLD -> 0
             property: mirax.LAYER_1_LEVEL_0_SECTION.USE_BLUE_CHANNEL ->
False
             property: mirax.LAYER_1_LEVEL_0_SECTION.USE_GREEN_CHANNEL ->
False
             property: mirax.LAYER_1_LEVEL_0_SECTION.USE_RED_CHANNEL -> True
             property:
mirax.LAYER_1_LEVEL_0_SECTION.VIMSLIDE_HISTOGRAM_DATA_CHANNEL_SIZE -> 256
             property: mirax.LAYER_1_LEVEL_0_SECTION.XDIFF -> 0
             property: mirax.LAYER_1_LEVEL_0_SECTION.YDIFF -> 0
             property: mirax.LAYER_1_LEVEL_0_SECTION.ZDIFF -> -1
             property: mirax.LAYER_1_LEVEL_1_SECTION.ACTIVE -> ON
             property: mirax.LAYER_1_LEVEL_1_SECTION.BRIGHTNESS -> -5
             property: mirax.LAYER_1_LEVEL_1_SECTION.COLOR_B -> 0
             property: mirax.LAYER_1_LEVEL_1_SECTION.COLOR_G -> 255
             property: mirax.LAYER_1_LEVEL_1_SECTION.COLOR_R -> 0
             property: mirax.LAYER_1_LEVEL_1_SECTION.CONTRAST -> 1
             property:
mirax.LAYER_1_LEVEL_1_SECTION.DATA_IN_THIS_FILTER_LEVEL -> FilterLevel_0
             property: mirax.LAYER_1_LEVEL_1_SECTION.DIGITALGAIN -> 0
             property: mirax.LAYER_1_LEVEL_1_SECTION.EXPOSUREPERCENTAGE ->
100
             property: mirax.LAYER_1_LEVEL_1_SECTION.EXPOSURE_TIME -> 350000
             property: mirax.LAYER_1_LEVEL_1_SECTION.EXTENDED_STEP_COUNT ->
3
             property: mirax.LAYER_1_LEVEL_1_SECTION.EXTENDED_STEP_SIZE -> 1
             property: mirax.LAYER_1_LEVEL_1_SECTION.FILTER_NAME -> Qdot605
             property: mirax.LAYER_1_LEVEL_1_SECTION.FILTER_REAL_POSITION ->
1
             property: mirax.LAYER_1_LEVEL_1_SECTION.GAMMA -> 1
             property: mirax.LAYER_1_LEVEL_1_SECTION.IS_MASTER_FILTER ->
False
             property: mirax.LAYER_1_LEVEL_1_SECTION.IS_STITCHING_FILTER ->
0
             property: mirax.LAYER_1_LEVEL_1_SECTION.MODIFIED_COLOR_B -> 0
             property: mirax.LAYER_1_LEVEL_1_SECTION.MODIFIED_COLOR_G -> 255
             property: mirax.LAYER_1_LEVEL_1_SECTION.MODIFIED_COLOR_R -> 0
             property: mirax.LAYER_1_LEVEL_1_SECTION.MODIFY -> ON
             property: mirax.LAYER_1_LEVEL_1_SECTION.STORING_CHANNEL_NUMBER
-> 1
             property: mirax.LAYER_1_LEVEL_1_SECTION.THRESHOLD -> 0
             property: mirax.LAYER_1_LEVEL_1_SECTION.USE_BLUE_CHANNEL ->
False
             property: mirax.LAYER_1_LEVEL_1_SECTION.USE_GREEN_CHANNEL ->
False
             property: mirax.LAYER_1_LEVEL_1_SECTION.USE_RED_CHANNEL -> True
             property:
mirax.LAYER_1_LEVEL_1_SECTION.VIMSLIDE_HISTOGRAM_DATA_CHANNEL_SIZE -> 256
             property: mirax.LAYER_1_LEVEL_1_SECTION.XDIFF -> 0
             property: mirax.LAYER_1_LEVEL_1_SECTION.YDIFF -> 0
             property: mirax.LAYER_1_LEVEL_1_SECTION.ZDIFF -> -1
             property: mirax.LAYER_1_LEVEL_2_SECTION.ACTIVE -> ON
             property: mirax.LAYER_1_LEVEL_2_SECTION.BRIGHTNESS -> -3
             property: mirax.LAYER_1_LEVEL_2_SECTION.COLOR_B -> 0
             property: mirax.LAYER_1_LEVEL_2_SECTION.COLOR_G -> 0
             property: mirax.LAYER_1_LEVEL_2_SECTION.COLOR_R -> 255
             property: mirax.LAYER_1_LEVEL_2_SECTION.CONTRAST -> 1
             property:
mirax.LAYER_1_LEVEL_2_SECTION.DATA_IN_THIS_FILTER_LEVEL -> FilterLevel_0
             property: mirax.LAYER_1_LEVEL_2_SECTION.DIGITALGAIN -> 0
             property: mirax.LAYER_1_LEVEL_2_SECTION.EXPOSUREPERCENTAGE ->
100
             property: mirax.LAYER_1_LEVEL_2_SECTION.EXPOSURE_TIME -> 350000
             property: mirax.LAYER_1_LEVEL_2_SECTION.EXTENDED_STEP_COUNT ->
3
             property: mirax.LAYER_1_LEVEL_2_SECTION.EXTENDED_STEP_SIZE -> 1
             property: mirax.LAYER_1_LEVEL_2_SECTION.FILTER_NAME -> Qdot655
             property: mirax.LAYER_1_LEVEL_2_SECTION.FILTER_REAL_POSITION ->
2
             property: mirax.LAYER_1_LEVEL_2_SECTION.GAMMA -> 1
             property: mirax.LAYER_1_LEVEL_2_SECTION.IS_MASTER_FILTER ->
False
             property: mirax.LAYER_1_LEVEL_2_SECTION.IS_STITCHING_FILTER ->
0
             property: mirax.LAYER_1_LEVEL_2_SECTION.MODIFIED_COLOR_B -> 0
             property: mirax.LAYER_1_LEVEL_2_SECTION.MODIFIED_COLOR_G -> 0
             property: mirax.LAYER_1_LEVEL_2_SECTION.MODIFIED_COLOR_R -> 255
             property: mirax.LAYER_1_LEVEL_2_SECTION.MODIFY -> ON
             property: mirax.LAYER_1_LEVEL_2_SECTION.STORING_CHANNEL_NUMBER
-> 2
             property: mirax.LAYER_1_LEVEL_2_SECTION.THRESHOLD -> 0
             property: mirax.LAYER_1_LEVEL_2_SECTION.USE_BLUE_CHANNEL ->
False
             property: mirax.LAYER_1_LEVEL_2_SECTION.USE_GREEN_CHANNEL ->
False
             property: mirax.LAYER_1_LEVEL_2_SECTION.USE_RED_CHANNEL -> True
             property:
mirax.LAYER_1_LEVEL_2_SECTION.VIMSLIDE_HISTOGRAM_DATA_CHANNEL_SIZE -> 256
             property: mirax.LAYER_1_LEVEL_2_SECTION.XDIFF -> 0
             property: mirax.LAYER_1_LEVEL_2_SECTION.YDIFF -> 0
             property: mirax.LAYER_1_LEVEL_2_SECTION.ZDIFF -> -1
             property: mirax.LAYER_1_LEVEL_3_SECTION.ACTIVE -> ON

Thanks,

-Kedar
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