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The optional step of reconstituting the BM of NODscid mice should result in an 80% uptake of the fluorescent 'donor' BM in 100% of the NODscid 'host' mice, however optimization of the TBI will be required to enhance the reconstitution in other non-immunocompromsed strains. If mice are unsuccessfully reconstituted they will get sick and die rapidly following the procedure, weakened mice may require additional food and water sources.
The ICW once finished should look like that seen in Figure 2Biv. It is ideal to have a ridge of acrylic surrounding the glass coverslip as this gives strength to the join with the skull. Perfect windows are reproducible and allow for repeated imaging for up to 8 weeks following their generation (Figure 2C). Images produced through these optimal windows will look as those seen in Figure 3Bi. Imperfections in the window generation will produce images of poor quality for example, air bubbles under the window will prevent whole fields of view being imaged, areas will appear dark as the air prevents the laser imaging (Figure 3Bii). With excess glue and acrylic on the coverslip there will be a high level of background fluorescence and areas of the field being blotted out as seen in Figure 3Biii, similarly if there is dirt on the window small dots of background fluorescence will be visible in the field (Figure 3Biv).
Success of ICW imaging is predetermined by the integrity of the surgical technique, however, even optimal ICWs can encounter problems during the imaging session. As such, a range and degree of clarity exists in the images generated as seen in Figure 3. The publication quality image portrayed in Figure 3C occurs when everything is optimal. Although it is not possible for all mice, it is feasible to expect 80% of the images generated to look like this. One of the major flaws in the current microscopy setup is the use of inverted lasers. Mice have to be positioned on their backs and this results in excessive stress and discomfort that may lead to labored breathing during the imaging. This produces a 'lined' image as the breathing interferes with the averaging that occurs during the imaging, whereby, each pixel row is imaged four times and the average of the four is displayed in the final image. Any movement during the averaging, such as that caused by labored breathing, will create an artifact that appears as a line on the image, as seen in Figure 3D. Mice that are insufficiently anaesthetized during imaging may encounter this problem also. The 'lined' effect can be decreased by limiting the image averaging to on, however this will in turn reduce the image quality and may not eliminate the problem. Alternatively mice can be repositioned or retried when breathing has normalized. The use of an upright 2PLM would negate this problem as mice could be imaged 'in the prone position'. An additional problem with imaging on an inverted 2PLM includes the limited accessibility for positioning the ICW once the mouse is on the microscope, and this leads to 'segmented' images like those seen in Figure 3E. Here the laser and coverslip are not positioned perpendicular to one another and as such the imaging occurs at an angle. This results in the generation of a 'segmented' image where the sides of the field of view are not imaged. The problem is easily solved with the repositioning of the mouse to ensure the coverslip is completely horizontal once on the head mount as seen in Figure 3Aii.
The model presented here was specifically used to examine the role of BMDCs in the vascularization of tumor tissue and demonstrates the ability to use three different channels simultaneously (Cherry, GFP, Far-red - Alexa647 and APC) making the CFP and SHG redundant for this particular story. We were able to image mice longitudinally for up to 8 weeks, studying the recruitment and integration of BM cells into the vasculature at a single cell level, with no detrimental effects caused by the window. This model demonstrates the ease of collecting dynamic information on the source and formation of vasculature and the interaction of different cell types of interest, previously lost through end point histological analysis.
| Step | Problem | Reasoning | Solution |
| 1.4 | Bone shatter | Blunt tools | Collect bone marrow form a fresh mouse using sharpened scissors or fresh scalpel blade, bone fragments will inhibit TV injection |
| 1.5 | Low extraction (low viscosity) | Bone endplates cut too distally; poor collection method | Bones should be cut as proximally as possible and collected with the bone inside collection tube to prevent splash back
Time should be spent to extract the BM maximally and with care
If necessary pool more than one mouse into 1 ml |
| | High Extraction (high Viscosity) | Low collection buffer | Dilute out solution with extra 0.1% BSA, split to three recipient mice up to 500 μl per mouse maximum |
| 1.6 | Bad Intravenous injection | Poor vasodilation and vessel visibility | Enhance dilation with heat lamp. Place mouse in tail vein restrainer with built in light source to aid access |
| 1 | Mice Sick | Infection | Sacrifice mice according to institution rules. Ensure tails are cleaned prior to injection and check sterility of extracted BM in culture |
| | Mice die | Poor BM uptake | Check % of fluorescent BM uptake of dead mouse.
Optimize TBI for strain of mice being used
Increase amount of BM injection (example use one donor mouse for two recipients) |
| 2.4 | Minor hemorrhaging | Dura breached during drilling | Pressure with gel pads and and continuous sterile saline wash |
| | Major hemorrhaging | Brain damaged by drilling | Sacrifice mouse according to institution guidelines |
| 2.8 | Air-bubbles under coverslip | Poor contact with cortical surface prevents proper placement | Remove coverslip and add extra PBS to float the coverslip onto the window to remove bubbles |
| 2.10 | Slippage of coverslip during gluing | Acrylic mass is heavy, placing pressure on the coverslip and moves the coverslip out of the way | Tweezers should be used to hold coverslip down while vetbond and acrylic is applied |
| 4.2 | Bad Intravenous injection | Poor vasodilation and vessel visibility | Enhance dilation with heat lamp. Place mouse in tail vein restrainer with built in light source to aid access |
4.4
Figure 3C | 'Lined' images | Labored or irregular breathing | Remove mouse from frame and allow to recover
Increase level of anaesthetic administered and adjust position to ensure neck is not overly flexed or extended to prevent breathing |
| Figure 3C | 'Segmented' image | Brain is not parallel to objectives | Adjust position of coverslip to ensure it is flat |
| | Vessel not visualized | injection not seen intravascularly | Redo injection into alternative tail vein, warm tail to ensure good vasodilation |
| | High background | Dirty coverslip,
Air Bubbles, Acrylic | Wipe coverslip with damp 70% ethanol cloth, do not soak as may penetrate under acrylic and damage the brain tissue |
Table 2. Troubleshooting. A guideline for corrective steps required for problematic areas of the procedures.

Schemata 1. Experimental flow diagram. This demonstrates the timeline of events through experimental steps 1-4. Mouse models are setup over a week, to ensure the BM reconstitutes properly, and are not treated with drug until day 7 of the tumor to ensure the tumor grafts. Click here to view larger figure.

Figure 1. BM Reconstitution.(A) BM extraction procedure i. Dissection of the hind limb bones. ii. Dissected femur and tibia from the hind limbs, cleaned and ready for extraction. iii. Bones with end plate removed and flushed through, demonstrating the white appearance of the empty bones. (B) Schemata demonstrating where lateral veins for injection are positioned in the tail.

Figure 2. ICW generation. (A) Aseptic setup recommended (B) i. Exposed skull surface reveals the landmarks required for surgery, ICW should be positioned on the right hemisphere equidistant from the bregma and lamda. ii. Periostieum lifted with lidocaine solution, ready for removal. iii. Dental hook required for the removal of the bone fragment generated with the drill. iv. Finished ICW with dental acrylic. (C) Three example windows demonstrate the reproducibility of the method.

Figure 3. 2PLM anticipated results. All images show green BM, red tumor, Blue (pseudo colored far red) vasculature. (A) i. Demonstrates the head frame which retains isoflurane flow inside the small animal irradiator. The 8 x 11 mm collimator can also be seen moving around through the gantry. ii. Mouse in the inverted positioned in the head frame required for imaging, moldable plastercine ensures all windows can be accommodated. (B) Demonstrative photos of the outcomes of problems with the window generation from i. an optimal window, ii. a window with air bubbles trapped underneath, iii acrylic spillage over the coverslip and iv. dirt on the window itself. (C) Highlights the problems that occur with imaging following successful generation of an ICW i. optimal imaging ii. breathing artefacts create a 'lined' image iii. coverslip not perpendicular to the laser generate a 'segmented' image. Click here to view larger figure.

Figure 4. Functional uses and adaptations of the Model. (A) CFP post imaging processing whereby GFP image is subtracted from CFP image to reveal the true CFP image that can be overlayed the other three channels in white. Green BM, Red tumor, White CSCs, Blue (pseudo colored far red) vasculature (B) Demonstration of the collagen fibers that can be imaged with SHG. Green Dextran, red BM, Cyan Collagen (C) i. VEGFTrap cells in vitro demonstrate the GFP signal produced with the VEGFtrap. ii. In vivo imaging demonstrates the VEGFtrap cells clearly and in addition highlights the ease of switching channels to demonstrate the system you are looking at. Green VEGFTRap + Tumor, Red BM, Blue (pseudo colored far red) vasculature. (D) Demonstrates the collection of Fluorescein in the stroma of the tumor and not in the cells directly, shown by the lack of green signal overlay with red tumor. Green Fluorescein, Red tumor. Click here to view larger figure.