Download Guidance for reading the scanned in situ hybridization images on

This site contains high quality jpeg images (~1-2Mb each) of each scanned in
situ hybridization slide as they will appear in the Jackson Lab Gene
Expression Database. Full resolution, lossless jpeg2000 images (~20Mb each)
for each image will be made available for download on our local server, but
require ~150 Gb of storage and were hence not feasible for review purposes.
The images were acquired using a Nikon Coolscan film scanner. This does not
have the dynamic range of a microscope. In order to more easily see
localized expression for some genes, it is useful to open the files in
Photoshop and modify their levels (under image adjustments: autolevel).
The naming conventions of the image files are as follows.
Whole mount e10.5 in situ hybridization:
Example: 0967d = XXXX P
XXXX= MTF number (0967)
P – Permeablization conditions
a = condition 1 (3’ proteinase K treatment)
b = condition 2 (30’ proteinase K treatment)
d = One embryo at condition 1 and the other at condition 2
Slide sections e13.5, P0, and cerebellum P7, P15, and P21:
Example: T0042111000 = T XXXX YZA BLL
T = Mahoney Transcription Factor (MTF)
XXXX= MTF number
Y – Mouse stage
1 = E13.5
2 = P0
3 = Cerebellum at different stages (all on same slide)
P7
P15
P21
4 = E10.5 whole mount
Z – Slide number for brains that require more than one slide to complete
1 = rostral
2 = caudal
3 = further caudal
A – replicate number
Some genes have multiple replicates
B – not used
LL – image type
aa jpeg
00 jpeg2000
included here
quality 10; size 100%
Lossless and large in size, but they are not